Some of the ideas, at least my comet idea, the powers are only linked to the comet in the manor in that that event changed things so other powers worked. People who use magic use magic, mutants are mutants, gageteers are gageteers, but the super power levels have been made possable by the comet. It's a catalyst, not the actual cause.
As for why there needs to be a unified background, well, for continuity of the world. Which is why we've decided not to allow for Aliens (Which, if you look at the vote earlier in this poll, was a fairly popular vote). The reason for the current alteration, well, it allows for the world to be mostly how we know it, with few changes, so players don't need to learn a long string of history to play. That may be good in a more private game, but we're opening it up for potentialy hundreds of players, and GMs. And with the open nature of a living world, where events can be shaped by adventures written by a single GM, there needs to be some sort of control and reference point.
You're right about the universes having a wide variety, but in the manor of some particular series, they are limited. Batman, for example, has no references to Aliens (at least as far as I know), at least as Batman alone (IE, not Justice League/Crossovers). X-Men is fairly limited to mutants only.
Hopefully that answers many of your questions
