I posted the following on the other forum in 08/08 - 8729.1
I just had a phone call about this subject which has a long history.
I did a search of the Piper maintenance manuals to see if there were any specifics; all but one mentions the carpet is installed before the rails.
Maurice Taylor suggested the rails need to be bolted directly against the structure which makes sense. I see very few complying with this recommendation.
The attached is a compilation of the references I found; there are many more. On the last page you will find a scanned photo of a 400 sales brochure showing a rail on top of the carpet. Check out the model in the back seat!
Matt