When comparing FireJail vs Flatpak, the Slant community recommends FireJail for most people. In the question“What are the best FLOSS Sandboxing Apps for Security/Privacy and Daily Usage, Linux?” FireJail is ranked 2nd while Flatpak is ranked 4th.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Advanced sandboxing
Pro No problem running graphical programs
Games and video-accelerated programs have no problems running in the jail.
Pro Very flexible with little overhead
Pro Cross-distribution
You can install flatpak packages on any distro you want.
Pro fast
searching, installing and updating are faster than others in my experience
Pro Doesn't bog system down like snaps.
Plus it's not proprietary.
Pro Application sandboxing
All applications are limited to a set of predefined permissions, enhancing privacy and security.
Pro A well-written documentation
Pro Flexible runtime management
You can install a lot of runtimes for different apps, making applications a lot more compatible while still allowing some applications to share their runtimes.
Cons
Con Hard to use
Not very easy to set up, may require terminal usage.
Con Primarily command-line driven
Con Bloated
Due to the way Flatpack handles packaging, this can lead to a large cache being created which quickly inflates to unreasonable sizes. Not only this, but using flatpack requires a large chunk of space to be reserved for it's own file hierarchy.
Con Difficult to export packages
It is difficult and convoluted to export installed packages and move to another system.
Con Doesn't work well with CLI programs
Invoking CLI programs can be a pain. From the weird reverse DNS package names to difficulty in easily managing container environment.