Hmm, I've never considered that. I suppose if you wanted to be extra-sure, you could put a diode on each line, to ensure that current only flows in one direction (away from each supply). I -think- you'd need to put them in reverse on the -ve lines.

Any voltage difference would be very small though, so any back current should be too (I -think-)

Giving each supply seperate tasks (ie, motherboard+Nubus on one, drives on the other) avoids the whole issue, so it might be the better bet.