I searched GitHub issues and didn’t find this, but I had to skim because I didn’t know how to properly narrow my search. I may have missed an existing issue.
Currently, if you tell a VM to reboot inside the VM, i.e. in a VM terminal typing # reboot, then it will shutdown but not start back up. I would like Qubes to differentiate a VM shutting down and power the VM back up when a reboot is issued in-vm.