Set it up for familiarity and consistency, according to what the user wants. I'm right-handed and have always used the right lever for the rear brake, but I also ride motorcycles and have never had a problem adjusting back and forth from one vehicle to the other.

I have set up left/rear bikes for users on request, and I have also rigged bikes with a single dual-brake lever for the dominant hand of the rider in question. Do what works for you.