The use case here is that I'm in a different physical location to the computer and want to remotely connect and run everything I'm working on on the remote computer in my remote window manager, including a browser and ide and terminal and so on.

Maybe I was too literal. The problem isn't executing the reboot command. The problem is logging in remotely to a computer that hasn't been logged into locally since it booted.

In particular the problem is that if I'm going to be remote for an extended period of time I have to ensure that nothing could interrupt the local session, and there's no fix if it does.