The best part is that instead of doing what Flatpak does (just blocking things and leaving the user unable to to anything) the system will prompt you for a decision.

No, Flatpak isn’t the problem here, portals for these things exist. The problem is that apps would have to use them, and unlike Apple, there’s noone restricting the old / unrestricted ways of doing things… So apps usually don’t port over to the portals.

Even where the unrestricted APIs stop working, like with screen capture and Wayland, apps are excruciatingly slow to port over, because they don’t get kicked from app stores for it, and because many users can still fall back to using the old system.