Ok, I think you get it but you are doing it backwards. Make the AI use the standard default units (not copies/custom units).
Copies for the Player's Team:
But for your player's team units use custom units. You can make them based the original standard units, by making duplicates in OE. Copy and paste the units in OE. Set the new unit to default unit data. Now your player's team units should look exactly how they do now - perfect. No problems there right? Copies! Got it?
Now for the allied units:
AI uses unit IDs. So when you copy an unit is makes a new ID for that unit. So when you make custom units the AI will not build them or use them the same way it normally would. In fact, it won't even try to create them in barracks because it is trying to create units with the original default ID. Now for the ally units, let us use the standard units but then change their models. Ok, now for example we can have a footman that looks like a grunt. The AI will use it exactly like how it would normally use a footman. So now your ally team can have custom units that the AI uses just like normal units. Change the names and any other data you like.