I know it looks a bit goofy, but the cheap solution is to wrap the side rails with hot water pipe insulation. The hollow black foam tubing.
NRS still sells the Inflatable Boat Cleaner that originated with Dan Baxter at B&A Distributing in Portland way back. This stuff really works too.
You dampen the area where the stains are, spray or sponge a bit of the cleaner on, wait 30 seconds, then use a scrub brush with coarse bristles. Wipe off and rinse thoroughly. It should remove 90% of almost any stain without much effort.
If you want to coat the underside of the side rails with something, I would mask off the joints with some 1/4" tape, and the allen head bolts too. That way it will still come apart.