Random works better, i think, because the crew is pressed for time and may be panicking, and the boarding team is actively trying to stop them. As for quickly emptying the fuel tanks, blowing a hole in your own hull is a long and storied naval tradition. I still think the defenders should get a chance (attributes+morale check+opposed roll) to blow the engines and/or magazine up.
But it's not random it's either it has some or it has none (and none in this fleet has any) cause the whole fleet is out of fuel and going back to their colony to refuel or something like that.
Either way instead of making NPR's ever get to 0 fuel it should be limited to like 20 percent of their max fuel then they should act like they have 0 and do the same as if they were empty but still have a minimum of 10 or 20 percent of their max.