Basicaly, you ask for an ord selection during re-arm that correspond to the availability in the arming base. Nice option to have, though I doubt HTC will give it a priority.
BTW, currently, the rearm pad will load unavailable ordinance if you had it when you took off. This way you can rearm in a fresh-captured and porked base and go attack the next one. Also, you can continue to bomb GV after they porked the ord. I'm not sure if this is good or bad.