This, I doubt. DiZ renounced any kind of dark (meaning messing around where he shouldn't) research a while ago.DiZ, also being the scientist he is, might have taken extra pod in case
he too decided to experiment with memories.
Yes, it does.DiZ taking extra pods
in case any broke down also seems like a valid reason for why he might
have brought a few spares.
I seriously doubt it would relate to BBS, though Castle Oblivion WAS around before the Organization found it, according to Another Report.And then there is that possibility that the
pods hold deeper meaning relating to BBS and Days (which I personally
don't believe to be the case)
As for the recently used pod, I persoally believe that DiZ placed Sora
in that pod when he transported him to the Twilight Mansion, since
those pods seems smaller and easier to transport. Plus the pod Sora
awoke in appeared to be part of the room's structure and not easy
to move because of both that and its size.
You have a good point there. The one Sora went to sleep in was small, but he awakens in a larger version. I think this will be explained in 358/2 Days, since it continues throughout CoM, and until the start of KH2.