I haven’t used any flatpacks, mostly because they don’t seem to have a good solution for running terminal programs. (Also I don’t like that the application developer chooses the permissions to expose rather than the user.
However, I have been using bubblewrap which is what flatpack uses under the hood to sandbox. This allows me to run both gui and non-gui programs, and I have the control of exposing the minimum required permissions that I’m comfortable giving an untrusted piece of software.