mainly it would be usefull for special external stores. maelstrom is a good example where you can strap a gargantuan meson torpedo to your hull on bank 3, and still get your nuke banks 1&2, missile turret, and gatling-howitzers reloaded by a support ship. with ballistics the flag is even more useful since you may want to allow the rearm of primarys, but not certain secondaries.
on the other hand a system where you can set a support ship's inventory, a list of ordinance kept aboard the support ship. so say you have gatling guns and missiles in the ship, but no extra warheads. so you can fire the warheads you have, but aren't allowed any more. take it a step further and you can specify quantities of weapons available on board the ship. so you can put 10 warheads on board, and bombers can reload them until their gone. something like this could do the same job, and better.
but the former solution seems like it would be an order of magnitude less difficult to implement. adding a flag and then a conditional in the rearm code. the latter option would require changes to fred as well, and more complex additions to the rearm code.