but if I want to use it to open a file that isn’t in “downloads” I have to use flatseal to give it extra permissions
There has been a portal to prevent this issue for years now. The fix isn’t to patch around issues in Flatseal, it’s for developers or Flatpak packagers to fix their security policies and code.
As an added benefit, KDE users get thumbnails in their file picker because they’re no longer stuck with the old GTK one but instead can use their native file picker portal. A win for everyone!