Glad to hear!
I don't see how this conflicts. What prevents the "promoted" unit from becoming the unique commander? As a matter of fact, some races can get free commanders as a bonus.
The reason I put "promoted" into quotation marks is because I mean the unit would be upgraded, via a spell. The original is killed, and the commander unit is created, perhaps with all/some XP of the original unit, and, as per the extra idea, unique promotion from the original unit's type to add even more strategic planning to forts.
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EDIT: I probably should elaborate. Say I build a fort. Then, I make a warrior in my capitol, which gets 6 starting XP. I march it over to the fort, and on the fort square there's a spell "Assign Commander". When I do that, the spell deletes the warrior, creates the race's appropriate commander, gives it (6*50%) 3 xp, and a free Battle Command I promotion for being a melee unit. A 2nd tier melee unit, say Axeman, could grant Battle Command II. An archer would give Defensive Stations promotion, a Recon unit would give Scouting promotion, a mounted unit would give tactics promotion, and a Great Commander unit would give Command Limit/Command Range promotions. So on for Arcane, Disciple, and maybe even Animal/Beast units (when applicable)
This could make it very complicated to code for, and to teach the AI to use it, though. I realized that as I typed it out
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The thought behind this relates to early game forts. A lucky scout/hunter can make it across the map, and suddenly I have a large cultural hold across the globe. In this mechanic, you have to either sacrifice the scout or march another unit across the aforementioned globe. This also makes them more of an investment, and less of a spammable object.
That's right! They do benefit from them differently, meaning that their forts may get/need varied bonuses from a Bannor or Goblin fort.