Regarding the problem of traits nd ancillaries being restricted to generals, the way to work around this is problem goes in line of BYG system ( BYG system allow only some generals to conducted far away missions. Armies without a general in a hostile territory will almost immediatly rebel).
Take the following situation: you are Epiros and you to attack Dalmatia, in this case you could place your army at the frontier (but in your home territory) and would not consume supplies (therefore there would be no need to micromanage in the way that you post). Now, you attack and conquer Dalmatia, you would be consuming supplies but most importantly Zagreb is a region with low order and separating your army from the general would dramatically increase the chance of rebellions ( even if the troops are garriosoned in the city or in a fort).
Second example: your are invading Syria from Spain, if the armies are setted to rebel when an army doesnt have a general (with permission to conduct foreign missions. Ex: Roman consul). It would be very diffuclt to avoid army consumption because your are far away from your home territories and separating your army from the general would lead them to rebel.
Instead you could use two general with the supply train ancillary set one in Cyprus - an ally territory for instance - have him buy supplies there and then supply the campaigning army or have the campaigning army supply at a ship (control of the seas will be far more important since they will support your army with the supply line).
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