Frellwit

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.)

Some links explaining this topic:

• https://gitlab.gnome.org/Teams/Design/os-mockups/-/issues/150
• https://gitlab.freedesktop.org/xdg/xdg-specs/-/issues/84
• https://blog.tingping.se/2019/09/07/how-to-design-a-modern-status-icon.html

The different heights could be related to your custom font or theme. Does it happen on defaults?