If you use baseurl to select the .onion mirror (or another specific mirror) it could occasionally be out of sync for a while. With metalink you’ll sooner or later get an up-to-date server from the rotation. You could select the non-onion master server using baseurl, but it might not be sustainable to have everyone use that.
BTW maybe it’s not Tor causing this problem with the mirror rotation but rather using a Whonix Gateway (e.g. sys-whonix) directly. I have a Fedora-based named DisposableVM configured as the system updatevm, with sys-whonix as its netvm, and I never experienced the slowdown on qvm-template list. Just now I tried with updatevm switched to sys-whonix, and indeed there it is… Edit: And it’s gone again :\