Gale isn't the only unbound Phoenix Weapon, or even the only one in the game.
Her Ki attacks, her body on death, and all Phoenix Weapon attacks (or attempts) we see glow the same shade of blue. We know that you have to be born with Ki abilities to use them, so chances are that Ki attacks in general can only be performed by Phoenix Weapons. But there are definitely other Ki users around - Aella is one, as she teaches Gale the Ki spear technique and describes Gale as "an even better Ki martial artist than [her]". The guards in the Daea inn talk about a former city guard who also knew the spear technique, and that wasn't Gale (and probably wasn't Aella).- And all of the ones on Earth are going to delay the alien war long enough for Gale to find a way to end it definitely now that she's in space
There's a yet unnamed interstellar power involved
The Galactic Federation wasn't supposed to have begun their attack yet, and Billy himself says that whoever hired the Kobolds doesn't want to be known.- Billy heavily implies that the Galactic Federation is being subversive in their invasion, but, considering his god complex and desire to destroy the Federation entirely, he may very well be wrong. Perhaps it's the aliens who invaded Earth the first time (and whom Billy states weren't part of the Federation)…?
Gale and the other Ki users are descendants of Phoenix Weapon 88
The intro had shown two bunkers numbered 66 and 88. One foreshadowed the appearance of 0066, the other was intended to foreshadow another Phoenix Weapon. And now that I think about it, when you go to the vault where the Ancient Armor and all the golems are, one of the golems is surprised to see a human and believes that the cryopod must have malfunctioned. This may have happened with 0088, who then wandered out to the rest of humanity and spread his/her enhanced genes.- Or it could be that they're descendants of the original Phoenix weapons used to fight in the great war. Or both, and 0088 was one of those Phoenixes.
Every time Gale dies is canon
One of her Phoenix powers is Resurrective Immortality. The Arcs and Harpies are designed after their mythological counterparts, so why not the Phoenixes?