[schmorptron]

In my experience you'll sadly still run into issues when running apps that weren't designed by the original authors to be used as flatpaks due to the permission issues you mentioned.

I see it as a necessary evil since a proper permissions system will make the attack surface for desktop apps much smaller in the long run, and the flatpak portals have the advantage of being much more visible and controllable by ordinary users than AppArmor or selinux (if there were even profiles) before them.