I cannot fathom why you'd try to defend a few of the holes in this story. It's one of those games you just need to take in stride and for fun and not overthink, because that's when it starts falling apart. It's not meant to be realistic.
Another silly, minor example would be:
Why Junko threatens them with the air purifier turning off when there's a large, healthy garden.
Also, since that one particular scene was mentioned, and this isn't really a plothole, just something that bugged me. . .
Remember how, after he gets out, Makoto was told he smells horrible? The next case started up before he
could take a shower, so there was no real time for him to even if you consider the type of storytelling where a game
may omit certain mundane events, like going to the restroom.
That entire time he was running around dirty and smelly and I couldn't take anything he said seriously.