I question why Native Americans cant be played in commander battle.
Good question. The answer is technical.
We have made A.I. bots replacing vanilla ones, but only vanilla ones right now. No first nations warrior bot for example. All commander battle units command-able depend on the very same type of A.I. bots you see when bots are enabled in-game.
So since the two type of AI types are interconnected it takes more work to make them useable for commander battle mode as commander battle bots are more integrated into the source code. This is a part of the MS (Module System) I am unfamiliar with, therefore I am also studying the source at the same time to better understand how it works exactly.