Yes you should be able to if you fool it into thinking the PC is on.
The M2 doesnt just give out power when the car is on, it tells the mobo that the car is on, you should be too. Then the mobo decides whether or not to turn on (via J8). This should be connected to your power button header btw. When the mobo turns on, it grounds pin 14 of the ATX connector (that big 20pin cable). This tells the M2 to start cranking and as long as pin 14 is grounded (to any black cable on there if your cable is standard, but double check first) then you will get all the correct voltages out. Once 14 is disconnected, those rails will disconnect. Also once the car is off, and the hardoff period is over on the M2, those rails will disconnect (like pulling the plug from the wall).