That is a flaw. Flatpak is great where it works but Flatpak doesn’t solve all problems, neither does any one solution except os level modification. It can be a last resort by it should be a last resort that works. The layering system could be put together such that you don’t get side effects of installing packages like that. It might be tough to fix but that doesn’t make it not a flaw.
If this guy could focus on what he’s good at and keep his damn mouth shut he wouldn’t be in this situation.