The earlier pipes have larger cones which is why I think they needed the indents. I can't speak to any modifications it needed since the bike came with them on it already. However, with a few minor exceptions, the CB500 and CB550 frames and most of the engine are identical. I would suspect that they are a straight bolt on application.
This bike has led an interesting life. It's a '73 CB500 motor in a '72 CB500 frame with '78 CB550 seat, pipes and sissy bar. Oh, and those horrid 12" over front forks. I'm 6'1" and I can barely touch the ground sitting on this thing.