With the two station houses on each side of the bridge, there's absolutely no reason why they shouldn't merge the #95E & #95W into the #95 again, from "The Plaza" to Buffalo (I didn't say bring the 83rd leg back though), with adjustments of the schedules/headways, etc. (the #381 can go back to their proper headways from State Street on west, with limited stops if necessary from State to Western). Merging the two would eliminate some of the bus flow going into and parked in the terminal. They can discharge passengers at state, and whoever wants to travel further (east or west of 95th, give or take) can do so. Pick up the passengers who's going further out and leave, just like the other east-west bus routes.
But even if you have that overpass, I strongly doubt folks will stop crossing the street. If they're really want to transfer to another bus an their bus is there, on the other side, they're not going to spends an extra minute going inside one station house, jump up some steps, run towards the over pass, go down those stairs, get out of the other station house, to get on that bus, and lets hope that bus doesn't leave at that point. Most likely, folks are going to cross that street on the other side, and get that bus.