SIGNAL SHUTDOWN (if configured in the Linux guest) will run the equivalent of "shutdown -h now", so as long as you provide the Linux guest time enough to execute a normal shutdown, it's safe to do that. 90 seconds may not be enough time - do a test shutdown manually to determine a rough idea of how long the system takes to shut down normally and add about 30 seconds for safety.
As far as startup, the system will run the normal startup scripts when autologged, so as long as the applications are configured to be started by init normally, you're fine.
