Oh I understand now, you’re referring to making AppArmor profiles to target a specific app. I just did a little research and it’s possible to create AppArmor policies for binaries that are in a user’s home folder.

Rather than hardcoding a specific user’s home, you can instead say “@{HOME}”. So you could create a profile for “@{HOME}/.local/share/flatpak/app/appID/current/active/files/bin/binaryName” that would confine the app for all users.