this is how it has to work in your car, the avic should be fine, however this could up the percentage of your unit getting a corupt file.
there have been a couple of ways to get around this,
one was to creat a device that would keep the unit powered up for a few seconds after power is lost from the acc being dropped during cranking. it would only need to stay powered for a second or two longer than what it would take at the longest for the motor to crank and start. i dont think that this is a good ideal, durring cranking, the voltage is much lower than normal, i think that this is far more dangerious to the system.
i would use a pulse timer decive to keep the unit from booting for a while after the power comes on (5-10 seconds) this would add of course to the boot time but would keep the device from being interupted during boot up and would also not let the unit continue to boot up while the voltage has dropped durring engine cranking.
most people dont do anything about it, its just part of owing a diesel. and pioneer would just be a big bunch of idiots if they didnt think about that (but then again, there always seems to be a bunch of stuff they do that just doen't make sence)