In VB6 you could actually force the game to never teleport commanders and you could only assign commanders if they were at the same location as the ship. You could still use the auto assignment function but only commanders at the same location could be assigned that way too.
It might be something Steve will come back to at some point.
As it says on the tin. . . Am I missing a purpose here?
You can manually pickup and drop off officers with ships. There's no real mechanical need for it at present. The only current purpose is for RP--I suppose if you don't like the instant-teleport of command assignments, you can move commanders around manually.