I’ve done some troubleshooting between Qubes (Fedora/Debian) and Whonix, and I can report that I know where it’s coming from, and it’s not a Qubes problem at all. For some reason, Whonix has set the $XDG_CURRENT_DESKTOP env to X-QUBES where classic Fedora/Debian qubes set it to XFCE (which is how they appear in telegram too).
This means that the solution to this is to simply set the variable to XFCE (/rw/config/rc.local):
echo "XDG_CURRENT_DESKTOP=XFCE" >> /etc/environment