All strats are still down for 180 minutes minus 4 minutes for each box of supps dropped at that strat. Do the math - that's 42 supply runs to bring up any strat object in 10 minutes. Your story is absurd, I guarantee you there are not 20+ people resupping strats late at night. And the strats are small enough that one drop will usually supply every object there, so if a strat goes from 33% to 50% it almost certainly. means the objects were destroyed at different times.
This has been argued to death many times before and the reasons Hitech did not make the change you want before apply just as much now: if you nerf resup, it will become too easy for a few guys in bombers to flatten 6 or 7 towns and spend the next 2 1/2 hours trying to sneak those bases because there's no way to resupply them. This will not result in more combat, it will result in LESS combat. It's all about unintended consequences.
I understand your desire to foster air combat but the fact is if some players refuse to get planes up and fight there is no way you can MAKE them do it. If they can't resup they'll bang away in manned guns or up wirbels and park on the runway . You see this all the time late at night, 2 or 3 people start to attack a base and instead of taking off there or better yet flying in from the next field you'll get a couple of guys banging away all night in 88s with no effect. And resupping is by far not the most effective way to defend a base, it's just the safest effective way for players who regard A2A combat as too risky. It's really only effective when combined with a more combative defense, otherwise the defenders will never get enough boxes to the town before the attacker can get one load of troops in unless the defenders outnumber the attackers substantially in which case they could more quickly and easily up fighters and kill the troops. But the main use of resupping towns and fields is to avoid the need to babysit them for another 2 hours after the initial attack has been beaten off.
As for not enough ammo to kill resupping M3s, most experienced base defenders know you need to let them get 2/3 of the way to town before killing them instead of blasting them the second they spawn. Any fighter in the game has enough ammo to kill 2-3 M3s and if you can't get troops in by the time they've made their 3rd trip only to be blasted 2k from town, you weren't going to take the base anyway. You might also want to consider having your troops on station before white flagging the town instead of WFing it and then having to bring troops all the way from the spawn or the nearest airfield. If your resources are too limited to have troops while town is still being taken down, get it to within 2-3 buildings and then come back with troops, the M3 with troops can get those last few with its pintel MG on the way to the map room (and of course the air cover could easily kill a couple too). Most defenders usually don't think about resupply until the flag goes white.