TheThis isn't really a gotcha. They're still naked because the game wants the player to ask what's the point of that (aka foreshadowing), which is explained at the end, but they still kept character identifying features like the pomp, glasses, bandages. This is all moot anyway because *endgame spoilers*that's just how they look in the simulation. The game never shows anyone except Juro and Megumi at the end coming out of their pods. We don't know if these other characters came out with their pomp or accessories or whatever.
You guys are putting way too much thought into this. Even if they made this more internally consistent, which I don't know why it matters, do you think they would rewrite this twist so they're not naked? I'm going to guess no.
grown in pods