The pratical problem is that Commander should have a cost that reflect theyre abilities, no matter how many units they goes to command. This is to avoid unnecessary complications when you choose you're force. So, giving a cost and saying there can be one every 1000 points can solve the problem, in an abstract way I agree, but if works...
It just seems arbitrary, that's all. What if my force is made up of 5000 points and each unit had "Disciplined". Maybe I'd want one or two commanders to bolster any individual units when they get poor rolls, but there's really no need to have the commanders there.
Then, imagine they're fighting a 5000 point force with mostly "Undisciplined" units. I might take extra commanders in this case.
As soon as we dictate the force construction, I'm afraid we'll need to make all sorts of concessions for individual problems that causes. And, at some level, then all the armies become the same.
You know the orcs are under-represented by commanders, there's simply not enough Orcs who want to risk their lives for command, but it makes them more interesting to command that way.
There should be a mathematical answer to this, hopefully Kevin will attach his spreadsheet so we can look at it (hint, hint)