I Herculined the entire floorpan of my rig and I love it. If your "system" is really important to you, you may find the Herc interior a little harder to live with. It does transmit more noise and heat than the old carpet and pad did. But then it was the carpet and pad trapping all that water that caused the huge cancerous lesion over my muffler and cat!
Since the Herc went in, I've beaten it, abused it, even spilled battery acid on it and it came away unscathed. No kidding - left an old lawn tractor battery back there for a few days until I got around to returning it for the core charge. It tipped over and spilled acid out in a puddle about three inches across. It ate a shop towel leaving nothing but one small corner and some red dust - but didn't affect the Herculiner at all.
Prep IS in fact the key. Follow the directions to a T, be careful with the Xylene solvent, WEAR TWO PAIR OF GLOVES and cover every square inch of your body that you don't want to be wearing Herculiner for a couple of weeks until it wears off (eyes, face, hair, arms, etc.). And not wimpy gloves either - good chemical resistant gloves that can stand up to the Xylene. Scuff down all the paint and degrease it twice. Do all that and it'll cover like a dream and stick forever. Brush in the corners and edges, then roll on two coats.
For the word on deep water forays - look for ForeWheeler and/or Vug to chime in.