If I understand correctly, what you're trying to say is engine crank, when your car starts the voltage of the battery drops. This is virtually eliminated by the buck/boost circuit on the psu, it'll compensate just fine. So basically, if your car battery is working fine, your carpc will work just fine.
Technically, if the psu is struggling it should go into some sort of protect mode, though I've heard horror stories of the M2Atx going on fire before. One way to check is to run a amp meter and check how much current is drawing from the battery by the psu, and if the value is >90% of the rated current, you're probably working the m2atx a little too hard.