as from Firefox RPM for example I can open any file and save anywhere. But its process isolation right?
For Firefox, the verdict on its native sandbox vs Flatpak's native sandbox doesn't seem conclusive. With -assumingly- knowledgeable peeps on both sides of the argument, which indeed does raise the question how knowledgeable they actually are. Nonetheless, for myself, I've accepted Flatpak's sandbox to not be inferior to Firefox' native one. Thus, I don't see any problem with using its flatpak.
Additionally, ensure that flatpaks are installed within that home partition. Some distros (like Fedora) default to installing flatpaks system-wide (and thus flatpaks end up being installed in
/var
instead). So, after ensuring that your home folder is correctly found within the home partition, just install flatpaks with theflatpak install --user *package-name*
command.