God-like powers? Check. Deity of Human Origin (the Linto Tribe)? Check. Power struggle for who actually gets to rule? Check.
Add into this that the conflict with the Grongi, according to expanded universe stuff, happened sometime during all this, and that Helhiem has been to Earth before according to Ryoma, and it's quite possible the Overlords had become Overlords, with either the Overlord of Darkness having the Forbidden Fruit or the Overlord of Light having scattered it throughout humanity along with his own essence when he died.
Shouichi being the only one to land a hit on the Overlord of Darkness makes him arguably the strongest Rider in the show. This coupled with the fact that the Seed of Agito is meant to keep evolving beyond the limits of normal humanity, Shouichi becoming a Deity of Human Origin wouldn't be far-fetched.
Shouichi is pretty much The Cape and knows the Overlord of Darkness's motivation, so it's possible he intentionally only damaged him enough to defeat him and end is spell but intentionally let him live. This would explain why the Overlord has a change of heart: he believes letting humanity evolve will spell his own demise when they overthrow and destroy him, so Shouichi sparing him would shake up that worldview.
