You can see an idea of lines where the old rail lines were on the flight deck when Kirk looks sorta that way when he boards the Enterprise in TMP.
Which we see the lines (which are very thin) in TWOK:
And a clearer view of the actual model taken as reference shots:
You can think of it as ST version of the RAST system. It could be a line of tractor beams designed to grab tight the shuttle to either guide it in or or out of the flight deck.