I'm a band-aid fix guy. I do my thing over in the corner and try not to contradict the main lore.
My Incarnates are all wielding part of an artifact that, like Excalibur with Hero 1, gives them Incarnate abilities. They started out less powerful than the signature heroes, so even bumped up they're not really on Positron's level.
As for the main lore? I kind of like that there's something where all the big brains of Paragon are stumped. That it defies comprehension. Everybody's scanning and aura reading and trying to nail down how the Well works and the answer just always comes back "We know it does work, but this is something that, if we did understand it, would probably drive us jibberingly, Lovecraftian levels of mad."