It would be a mess for sure. You have to do the sync before the reboot or it would really freak out with a v6 config loaded on a normal system.
Now that I think on it more, I'm not sure if the gitsync-on-update code accounts for having to install the files on the second NanoBSD slice either, so that wouldn't work at all either way.
You might be better off waiting for databeestje to make new nanobsd snapshots, and then just gitsync from one of those manually after installing/upgrading using them.