It's all too confusing as of now, I mean there are so many things that are either not complete and confusing us or there's a reason behind everything, for example, I was noticing how Marluxia is not a Nort since he lacks the traits of a Xehanort and yet Larxene IS, BUT Larxene despise having those iconic Amber Eyes, she has no pointy ears 'nor Silver Hair, however Aqua does have the traits EXCEPT for the pointy ears. Xigbar did say once "Me? I'm already HALF Xehanort" but he has no Silver Hair at all, just the eyes and the ears so it's quite confusing as I said.
Regarding your theory it's possible but there are some things to consider such as the time differences in The Realm of Darkness compared to the Realm of Light, if Xehanort used this in advantage to get hold of Aqua for example. Young Xehanort does say in Toy Box "There's a Darkness we are missing and must reclaim" so the spot for Sora not being filled and your theory on this aspect might be correct but also remember that in DDD he said "another on your list" while he thought he had Sora for sure as the 13th, so if he referred to Terra and then Sora was saved then the 13th darkness spot was missing so he could as well STILL have Terra and then got Aqua. The scene you mention with Riku and Mickey returning can as well be after the KH 2.9 scene where they return to change on their new clothes rather than returning from their mission, if you think about it it's more accurate but your statement is a possibility as well. It's a matter of times as if the Aqua stuff happened before or after that scene. Only time will tell.