- Edited
I am just a N00b and I am no security expert. I am not saying that flatpak is inherently bad, but my understanding is that it could be used in more insidious way to run code or access resources that otherwise wouldn't be allowed.
As much as I use VM, hypervisor can also increase the overall complexity of the system. I would personally not assume that the hypervisor is hardened by default. I personally would not enable features like shared memory or shared clipboard if there is a need for more security; these are likely not the most important but they might be overlooked. Some hypervisor likely do better than others in term of hardening but I would suggest to read the manpages. Some hypervisor may also come with unnecessary packages, or lack features as provided by the package manager. It's on my to-do list so I can't speak too much for it. There are likely 50 other areas to harden first or I might have underestimated its importance.