Keep in mind that the deity Antonidas the Drevin has a description of the how the world was created; for the moment, that creation mythos stands as the only one (that I'm aware of, at least), but I see no issue with multiple conflicting creation mythoi.
In my own campaign setting, there are several different creation mythoi, all of which pretty much conflict; no one is really sure how the world got there, though priests are all pretty convinced that their particular faith's method is how things went. I see no problem with having conflicting mythoi in LEW; in fact, if anything, I feel that it would further give the setting a feeling of uncertainty: sure, the world is here, and there is probably a way that it was created, but we have several possibilities, so which one is right? With multiple, you can't ever really be sure.
I would agree that deities that don't really have followers would fall into the "overdeity" category. I don't see an issue with having deities of that classification in LEW, and I don't see a direct effect on the setting as a whole; the effects of these deities is more wide-reaching, yes, but is also more subtle. However, introducing overdeities brings the gap in deities to the forefront (a ton of lesser deities, some intermediate, one if any greater, and a few demigods); the majority of the deities being "lesser deities" would have to somehow be explained.
Overall, I really like the idea of the opposing forces in the world be "creation and destruction" as opposed to "good and evil" or even "law and chaos." However, their alignment should be worked out (El Jefe had many good points on what their alignments *could* be); I personally have no preference, so long as it ends up being clear what their alignments are.
Their relationships with the existing deities should also be pointed out; they may be distant, yes, but I'm sure that some of the deities have had at least indirect interaction with them, and are probably aware of them. Even a "this deity has no interaction with this overdeity" would work, but some idea of their interaction would be good.