@zjuhasz1 Right, this is also fixed. The packages were installed because we use apt without --no-install-recommends. You can remove those gnome packages by hand for now if it bothers you but it doesn't run any daemons, so it's mostly harmless.
@girish my initial questions are all resolved now. I'm having some new problems though. Namely that it seems the Cloudron installer is installing Gnome which is making my server enter sleep mode. I disabled it now but I'm confused as to why Gnome is being installed.