I got it to work. I fully removed snap/snapd from the appVM with:
Stop snapd services
$ sudo systemctl stop snapd
Remove snapd packages
$ sudo dnf remove purge snapd gnome-software-plugin-snap
Remove user snap directory
$ rm -rf ~/snap/
Remove cache directory for snapd
$ sudo rm -rf /var/cache/snapd/
Afterwards I installed snapd and the qubes snap helper inside the appVM and restarted.
I left the fedora-32 template how it was because the template itself worked fine.
Now installing and running applications inside the appVM worked fine.
Not sure why it didn’t work in the first place. I might have done some miss cofiguration or snap had some sort of “hiccup” 
.
But I still don’t really have an explanation why everything worked perfectly fine inside a standaloneVM (I read in another thread that running snap inside standaloneVMs causes less problems) but I would like to understand the difference in doing so.