I can't say with any specifics but flatpaks are sandboxed on purpose, when you override something you're giving it more (or less) permissions than the developer thought they'd need. "Automatically giving permissions the developer didn't think they'd need" seems like a crazy thing to try to automate, no?
Check out Flatseal if you haven't already. It's a GUI for flatpak permissions. Might make your life easier in the future.