I think it would be good if they expanded the permissions system. Taking inspiration from the android world where it will ask for the permission whenever it needs to access something on the system. This is an ideal world but would take a lot of effort for the maintainers to implement. I guess it needs time to mature. I just hope flatpak devs want to adress the issue eventually… So far I only ever see people just accepting the way it is now and finding workarounds…