Which app? Because it all depends of how much access and permissions the app needs. Managing volumes or changing devices is usually the problem. So far I've only had to layer two apps (on bazzite, though): veracrypt and vorta. To access old backups. Everything else works fine, even desktop integration. Although I prefer to use box buddy to handle distrobox as a UI, which runs as a flatpak without problem. It's been great so far at resolving that kind of issues: bug, update, now it works.