Because the user getting a hundred popups on app start for various files the app needs isn’t exactly a usable experience

It doesn't but until apps can declare on a simple config file what paths they require that's the way things should work. I guess that would motivate the developers who are packing into Flatpaks to properly list whatever files the application requires. If they don't, then the application will still work fine but be a bit annoying.

Also, blocking the app’s main thread (which is the only way you could do this) is likely to break it and cause tons of user complaints too. Aside from apps using the APIs meant for the purpose of permission systems, there’s no good way to make it work.

Yet, macOS does and things don't go that bad, on the example how do you think they do it for command line tools? The system intercepts the request, show the popup and wait for the user input. I've seen the same happening with older macOS applications that aren't aware it could happen and yes, the main thread is blocked and the application seems to crash.

I thinks it's way better doing it this way and still have a somewhat productive container and isolation experience than just bluntly blocking everything - something that also breaks apps sometimes.