The scanner is always in Serial Port mode unless it's in Mass Storage mode so no need to do anything to put the scanner in Serial Port mode. The problem with a computer reboot is the serial port driver stops communicating with the scanner after the computer reboots.
If using ProScan, you can send the MSM command to the scanner before the computer reboots. That way, after the computer reboots then the scanner reboots and all should be good.
No way to turn on the scanner from the computer because the scanner is off and therefore no serial port comms. Like I said, send the MSM command to reboot the scanner.