Except the problem here is that those "inconsistencies" were already explained away. We could reasonably figure that when the worlds got reset by Sora in the first game, its form got reset as well. Notice how in the first game, it was oozing darkness and infested with Heartless until Sora was all like "ZA WARUDO" and KH decided to turn on all of its lights.

My leaning is that you're onto something, but it's largely unimportant, unless Mister Master Man's ability affects how KH is perceived by those who get close. If it does matter, then noticing means something. If not, then it just gives us an in-universe explanation for a possible designer oversight that can be applied after the fact. Either way, insignificant unless shown to be otherwise.

Not that we should discourage any sound theory based on evidence and a little bit of rationality.