Just as the title says, maybe it could be possible to edit a custom campaign map so that multiple Commander Units can be controlled during the same level.
This can be done on Campaign maps! Unfortunately, due to a lot of reasons we're still ironing out and fixing, they can't be done with usual skirmish/scenario maps. But, if you go into Create Campaign > Place a mission tile > Edit > Player Properties and select a commander, you'll see a check box that says 'Independent'. If you un-check it, the commander selected will be assigned to the above commander and players can use them just like any other unit. Let me grab a screenshot.... Unless I've misunderstood the suggestion?!