Successfully reproduced the issue on Manjaro KDE. (Curiously, neither Fedora KDE nor Kubuntu 24.04 has this problem.) After a bit of inspection, it looks like something is corrupting the partition table on the workstation, specifically by corrupting the value that specifies the end location of the root partition. I’m not entirely sure why yet, but that seems to be what’s happening. (Maybe systemd-repart is misbehaving?)
edit: Gah, I was able to reproduce this one time and now subsequent attempts to reproduce are failing. Will need to do more research on this later. For now, my advice would be that if you encounter this, try deleting the Whonix-Workstation VM entirely, then define it from the XML file and copy the qcow2 image to /var/lib/libvirt/images as described in the documentation. On the first boot, boot into “PERSISTENT Mode | SYSMAINT Session”, then install updates from there and reboot into a user session. It’s possible this is a semi-random glitch.