I always check my flatpak settings post install before running the app and adjust permissions according to need. I mean it does offer more security to me since it’s user installed, I can granularly update permissions and control more or less where and what is can touch.

Alternatives to this are SELinux,AppArmour and firejails which are slightly more inconvenient to use.

To me that is mostly secure,or secure enough.

Well and then there’s some immutable distros which might help overall.

Edit: paragraphs