I have two 500s. One with original 4/4 and one CMS/DS pipes.
Just looked and my bike with the DS pipes the run of no 4 pipe is about 1/4 inch further out than my Honda system. The brake pedal gets close when full depressed. The pedal undepressed is sort of level with the peg and that suits me, but if it were adjusted down it might well hit. The mounting plates used for the DS exhaust were the original and were a bit bent, plus the point where they mount to the frame on this bike looks also a bit out. So this may have some bearing on this.