On Ubuntu I use the tar.bz2 version to not have to deal with snaps or extra repositories. Also on Debian Stable to get the latest version.

celluloid, pix, hexchat, hypnotix, rhythmbox, LibreOffice

Those applications uninstalled just fine without any dependency issues last time I tried Mint.

If you’re unsure, make a snapshot of your current VM state (if your VM software supports it). Then just uninstall the junk you don’t need until Mint breaks. Restore snapshot, test some more, and so on. Those on real hardware should use Timeshift to create snapshots.

Tip: Run sudo apt autoremove package in the terminal so you can see which dependencies that are removed.

You shouldn’t have to install any flatpak dependency manually. Flatpak should handle it for you automatically when you install your programs. (In most cases.)

OpenSUSE use patterns. Groups of packages that can be selected during installation. If one of the included pattern packages is removed it will be “fixed” when updating. You can uninstall some patterns, but be careful as some may be more important than others, leaving you without a graphical interface or something like that. If you decide to do a reinstall, you can deselect a lot of patterns (search for “pattern” in the software selection section of the installer).

Is there an equivalent or something similar to “Use host i/o cache” that VirtualBox have? Last time I tried virt-manager the install time of the vm was incredibly slow because of the terrible write speed to my hdd. Vbox fixes that issue with the host i/o cache setting.