That is still a bit beta... at the current state the DC simply switching you ship to full AI control. None of your ship systems can be used by the pilot while docking. I think this will be improved over time. I hope they implement Sarahs solution with the fix for the return to the 1km point while flying already near the pad at outposts.
I recall the programmer saying that it's a bit of a hack and it'd be a bit more work to make individual controls like the lights work manually while on computer control.
Thanks for the replies & info.