This is the current problem.
Destruction has 200 players in oRvR across three zones.
Order has 100 players in oRvR across three zones.
Order has 80 players in Caledor trying to push for fort.
Destruction just needs to move all their forces to elf, get to a three star keep and leave 2-3 warbands there so Order cannot realistically take the keep. Destruction can even leave no people and just zerg Caledor whenever order pushes for a keep. In either case, order don't get an AAO bonuses to their RR.
Destruction can then stick 50 players in dwarf zone and 50 players in empire, and get two star keeps in both against no opposition.
With me so far? Lets say Destruction starts a seige in Reikland. Let's say Order rallies, moving from Caledor and expels Destruction from the keep after a big battle for the inner keep. Maybe the outer door and inner door are destroyed, and need repaired. In the meantime, destruction seige both Caledor and Kadrin Valley since all the order players are in Reikland now.
Order rush to Kadrin Valley and fail to win the seige, A fort gets triggered in Kadrin Valley, so we have a fort in Stonewatch. There is 40% AAO in Stonewatch. Reikland is lost after a breif battle since all of orders forces are in Stonewatch. Reikwatch fort is now 50 v 11 in destruction favour. They take the fort in minutes because all they have to do is kill an npc lord and a handful of players. Destruction then move to Stonewatch where AAO is 100%.
I could switch "Order" with "Destruction" there, and the same problem will exist. If you think the outnumbered side (Order in my example) has some strategy it can deploy, I'd love to hear it, because they don't even seem to benefit from AAO any more. I don't disagree that the way flags are captured might help things, but the issue is not really being caused by supply run mechanisms.