I agree with the sentiment; I also want to control where things are installed. But the framing of the technical problem here is totally backwards. The operating system or application manager within the operating system (what does flatpak consider itself?) should decide where all application state goes. The application shouldn't ever prompt the user for this, it should just assume a path inside a sandbox. That path in…
Spoken like a Linux software developer, I suppose. As a Windows user of generic software (image editing, video players, games, etc.), I want to be able to control such crap. I have a media player that can easily fill a small HD with its mindlessly huge DB, for instance. Rather than manually cleaning periodically, or upgrading my $y$tem, it's easiest to say "Software, store your data here ".
These techniques are pretty general purpose. They aren't merely a cultural artifact of Linux or FOSS. Anyone trying to sanely deal with authorization is going to stumble upon sandboxing, and capabilities, and the principal of least authority, etc. if they look hard enough.