I dug around and found out a few things.
If I understand what I read correctly, it looks like the Commander does do the actual flying, while the pilot is really the co-pilot.
I am guessing the CEV will operate the same way.
I can see how such an arrangement evolved. With limited space for crew, each crewmember would wear many hats. And it makes sense to make the main pilot the commander.
As ships get bigger, and crews get bigger, I wonder if we’ll see a separation of those duties- a main pilot and an actual commander? It will be a long time before ships get that big IMO.