The s4 guys do not HAVE to do that. I was researching ERs and know the thread you are speaking of. Something was wack with that guys car... there are plenty of others that had no problems during install.
A6s have the most room of all 3 (A6, allroad, S4) there should be no cutting of the frame rail. I spoke to JHM for over a half hour on this, discussing examples of what people had done etc. They swore up and down there was no cutting of the frame and they said at most there was only some minor trimming of the shroud.