Well, the out-of-spec (low) voltage is easily solved. As you suggested earlier, just use a higher voltage input to Vin. The 12V from the car itself will work, but will also generate unneeded warmth.

Pretty much any DC-to-DC voltage converter will work -- there are tons of them on eBay for about a buck apiece.

The Arduino Mega schematic has some circuitry around the Vin/USB parts that looks like it is intended to cut out the USB power when powered from Vin. So it _might_ actually be safe as-is. I just found it a bit odd to measure 5V at the (unconnected) USB connector when powered via Vin. And the slight reverse current I measured isn't enough to worry about, so long as it stays that small.

Perhaps I'll try a couple more experiments with it and see if I can uncover evidence one way or the other.