Hence their gender ambiguity. Also in such societies birth of hermaphrodites were considered bad omen, so they were likely ostracized most of their pre-Overlord life. Until they claimed their power and instated absolute gender equality.
Possibly that's how they became the Overlord: they resolved some sort of ancient Edict with conditions along the line "neither man nor woman" or some such to gain initial power base.
Kyros is the last survivor of the ancient civilization that created the Spires and the Oldwalls
That civilization destroyed itself in a series of senseless conflicts and abuse of Edict-level magic. Kyros' conquest is driven by a desire to create a world order to replace their lost civilization, and their laws, especially those against forbidden knowledge, are meant to prevent people from destroying themselves again.
"Bastard's wound" implies they're built by ancestors of the Beastmen before they degenerated into current form. Though Kyros could be one of them.
Kyros had every intention of having you "take over" the Rebellion
By historical analogy, Kyros runs the Roman or Achaemenid Persian Empire (her name even sounds like Cyrus the Great). Graven and The Voices are unsuitable viceroys (one being a foreign oppressor and the other clearly just batshit insane). But a loyal Fatebinder who binds the former disparate nations (handily destroyed by the first two Archons) of the South into one satrapy that can be left to run by itself while she focuses on the rest of the world? My, doesn't that sound like something a wise overlord capable of conquering the whole world would do?
This even fits with the storyline for the Rebellion. You're still pretty bloody evil when you do this run ( murdering babies tends to be frowned upon in polite society) and you end up running the whole region through many acts of murder (and, because of the conquest prologue, betrayal). Kyros appears not to care whether the land is ruled by her through subterfuge or force, just that it is ruled by her!
You can be pretty bloody evil, but you can also be nicer than the example. You don't have to murder the baby if you have the right stats or the right knowledge, and can loophole out of it to achieve your not-actually-evil goal without babykilling.
Kyros's original plan was...
...not at all how it turned out. When Kyros proclaimed that only one Archon can rule the Tiers, they expected Tunon to win. Bleden Mark would immediately bow to Tunon due to their long-standing friendly relationship. Graven Ashe and the Voices of Nerat would attack each other and the winner of that fight would then attack the Fatebinder/Archon of Spires. Bleden Mark would kill the winner of that fight while they're weakened by their two previous victories, with Sirin getting offed along the way as a target of opportunity by somebody. Even if nobody kills Sirin, that leaves Tunon with only two potential rivals, both of whom he's completely immune to and could kill with ease unless they do exactly what he says (as he knows a technique to kill Bleden Mark with his own powers and he's immune to Sirin's voice). Kyros is thus free of four, potentially five troublesome Archons (the elderly and increasingly unreliable Ashe, the traitorous and maniacal Voices, the subversive wild-card Fatebinder, the dangerous and capricious Sirin, and possibly the chaotic and unpredictable Bleden Mark) and rewards their only truly faithful servant with an entire realm (conveniently destroyed in the infighting) to rule knowing Tunon will immediately reinstate Kyros's Laws anyway. Kyros would get everything they want. Almost anything the player does makes them a Spanner in the Works because of this, and at their best can make it completely backfire by uniting all the Archons (with the exception of Ashe) against Kyros.
Kyros intended the Fatebinder to die, and the Edict of Execution to come to pass.
Kyros' expected scenario: the Fatebinder explodes or otherwise dies horribly from delivering the Edict of Execution, the Disfavored and Scarlet Chorus spend the next eight days accomplishing absolutely nothing but doing more damage to each other than the rebels do, the deadline arrives and the Edict of Execution kills everyone in the valley. The Vendrien Guard is squashed, Kyros is now rid of two potentially dangerous Archons, and the rest of the Tiers is terrified into compliance (as shown in the Bad Ending).
Except, the Fatebinder survived reading the Edict. Then they took Ascension Hall, whether for one of Kyros' armies, the rebels, or themselves, breaking the Edict either way. And now Kyros still has a problem with their Archons and other rebellious Tiersmen.
Kyros is a legacy character
The best known Kyros is male. The current one is female. And guess who's next in line?
Sirin didn't really see Kyros in the flesh
She met a body double of Kyros, and Kyros ensured that particular body double was the only one Sirin saw so she could think was the "real" Kyros.
Whether in their "true" form or some sort of shape-shifted disguise, a minor character (or several!) the Fatebinder has encountered was, in fact, Kyros, observing their conquest from the ground.
A related WMG is that we might not have seen Kyros... but we might have unknowingly communicated with Kyros in disguise as a bit character — Myothis. It would hardly be a problem for Kyros to write letters pretending to be a (real, but retired) Fatebinder that you've never met and would not expect to meet, and while it wouldn't let them observe the conquest from the ground, it would give them another source of information on your plans and way to manipulate you...
Kyros granted you the power to declare Edicts of your own.
While it's definitely possible that public perception of you just happened to grant you the power to declare Edicts at just the right moment, Myothis's missives about why Kyros hasn't taken you out by this point suggest that she has chosen to support your efforts. At the time, your base of operations is being attacked by a huge force. You don't stand a chance against those numbers unless you have something very powerful—say, an Edict—to level the playing field. Rather than show favoritism, though, Kyros simply activates the Mysterious Device at just the right time and lets you figure out what to do with it. If you figure out how to declare an Edict, then Kyros's intended Archon of the Tiers makes a clear show of force. If you don't, then the only person who comes even remotely close to posing a threat will die. Kyros has worked very hard to keep his connection to the Spires a secret, so it's perfectly plausible that she knows far more about them—as well as how to control them—than you do.
Kyros was the previous Archon of Spires and died shortly after the Edict of Execution was written.
The power of Edicts seems to be associated with the Archon of Spires, and there can only be one Archon of a given thing at a time. Since Kyros was the only one known to ever issue Edicts, that would make Kyros the Archon of Spires at the start of the game. The Fatebinder inheriting this position after Kyros's death could explain why they have so much power over the Edicts and how they have the ability to simply buck Kyros's authority - They're essentially the inheritor to Kyros's own power. Their power doesn't begin to show until they read the Edict of Execution, which would mean that Kyros would have had to die between the reading of the other Edict the player read and the time they read this one in order for the Fatebinder to be its inheritor. Since the Edict was already prepared then it would still have all its power, especially since it's being issued by the then-unknown new Archon of Spires, so nobody would initially realize anything is wrong until the Fatebinder unexpectedly survives reading it. But how could Kyros die without anyone hearing about it? There's a surprising number of cases where the overlord of a large but efficient empire can just die and nobody hears about it for a while simply because their empire is running so smoothly that the Overlord's input isn't needed for much, and Kyros has designed their empire in exactly this fashion. By contrast, there would be a large number of people well positioned to make sure nobody finds out and with good reasons to hide it, especially the older Archons like Tunon and Bleden Mark who derive all their power and authority through their relation to Kyros. Which would be precisely why those two will always try to gang up on the Fatebinder - If word gets out that someone else has Kyros's powers it might begin to make them question where Kyros is to stop it.
Two things that might be relevant is that the Fatebinder is proclaimed (by someone in a position to send Kyros' mail) the Archon of Edicts and there's a hint that they actually have more control over their Edicts than Kyros (Kyros apparently can't end an Edict without the fulfillment of the letter of the Edict by the discussions we have on the matter, while the Fatebinder either can do just that or is much more able to put in 'or upon the wish of the Archon of Edicts' clauses based on casually being able to end their Edicts while at a Spire).
Sirin's helmet has a way to be safely removed, for entirely mundane reasons.
Sirin's helmet functions as a Restraining Bolt to make sure she doesn't use her powers against anyone Kyros doesn't want her to, and it can't be removed without killing her. But it has to be able to be removed without killing her, simply because it's on her head. Her hair isn't going to stop growing and her skin won't stop being skin just because she has a helmet on, so they need a way to take if off so they can shave her hair and treat any potential rashes, infections, or diseases that would naturally spring from wearing one item 24 hours a day for multiple years. Also, since she's too young to have fully stopped growing, the helmet would need to be occasionally resized to fit her head. So there has to be a way to safely remove it, which Kyros likely knows and nobody else has found yet.
When asked about her history, Sirin mentions that her vocal cords were put into stasis, and there's healing magic. It's entirely possible the headdress has secondary enchantments to keep her hair from growing and to heal her skin.
Or, being a card-carrying Evil Overlord, Kyros just skinned her alive and grafted the thing directly onto her skull, then healed what's left.
