When I request a different runway after receiving taxi clearance, PF3 will naturally approve my request; however, I've noticed that the taxi guidance instructions it provides are still to the original runway. Also, it seems to reset my departure clearance once it gives me takeoff clearance. (There have been a few times I've missed this and then gotten yelled at in the air when I exceed that new altitude clearance because it was lower than the one I intially received.)
This is in P3D v5.3 running PF3 3.20.0.