When running 'guix system init', GRUB requires a GC root to be placed in /var/guix. When building a VM, this GC root is placed in <disk>/var/guix/gcroots however while building a system on another drive, the GC root is placed on the host's /var/guix/gcroots , not only overwriting the host's grub.cfg which could be problematic if GC is run and the host has a different grub.cfg to the system being inited, but the system being inited lacks the grub.cfg and can run GC and clear out its GRUB files itself.
'guix system reconfigure' once you're inside the new system fixes this issue for the new system, but the host system may still have a broken grub.cfg and will need reconfiguring also.
