So the challenge in reducing noise is twofold: first you have the transmission of the noise energy and second you have the energy of the impacting particulates.
For transmission of noise the less dense plastic inner fenders are likely superior. Rubber mounting of the inner fenders, while impractical and with structural drawbacks, would isolate and reduce sound energy transmission from the inner fenders to the firewall (and thus passenger compartment). Next down the line on transmission is the natural frequency of the parts. Thin sheet metal will tend to vibrate at a higher frequency on it's own. But make it thicker and the frequency drops.
For energy of the impacting particulates you can affect the amplitude and duration of the energy transferral but not the amount of energy transferred. This leads to the problem with Line-X type coatings: they are relatively hard. So they, like the raw metal, transfer all of the energy in a short high amplitude pulse. Think PING! Whereas a rubberized coating would absorb the impact leading to a longer and lower amplitude pulse. Think THUNK! For many humans the thunk is less obtrusive/annoying than the ping.
Thinking through this I would use a rubberized coating on the wheel side of the inner fender. I would also try and get a bit creative and use the rubberized coating on the contact points to the body.
I don't find this contrary to PT at all, if it wasn't rocks it would be rain. The idea of PT is modern convienience and features in yesterday's styling. Making your ride quiet or "tuning" the acoustics for just the right driving experience is *very* modern.
