Is the rail stainless? Aluminum? I thought stainless, no matter. If you get against a piling with it, regardless if it's bolted flush up against the fiberglass, or has 6 inches of rubber behind it, it can bend. The glass part is insignificant, it would matter little if it were bolted to titanium, it'll still bend.
The rubber will make up for the differences in the gaps that WILL be there, because there is no possible way that it will bolt up flush against the boat, unless it has screws about every two inches, and probably not then.
It had rubber between them initially didn't it?
And that's also why I said seal it with butyl.
it didn't have rubber, it had foam tape. and your right, butyl will probably work. i have never used the butyl tape. as good as it may be, i will never recommend something I haven't tried...
and why wouldn't a straight piece of aluminum not fit against a reasonably level surface... I have dealt with many, many rub rails on fiberglass boats and they all can be fitted snugly, not water tight, but nicely to a boat
along the top edge of the rail... sometimes the way the hull and deck are fitted makes it impossible for the lower edge to fit like it was designed to...
if the rail is installed properly, and up against the fiberglass, it will be substantially more durable than if it has a rubber cushion behind it holding it away from the fiberglass....
one reason is... if it has a cushion behind it, you will never get the screws/bolts tight without dimpling the rail where the fasteners are because the fasteners will compress the rubber.... and it wont be compressed where there are no fasteners.... maybe if it had fasteners every 2 inches it would be better. (it should have a fastener every 3 to 5 inches)
reason 2 is, if you don't get the bolts reasonably tight, and the rail is floating on rubber, as soon as you get against a piling, it wont only bend it inward, it could very easily pull it up or down a little..... not much but enough to make it ugly.... or it could get a sliver of wood under it and rip it loose.
reason 3 is, with it bolted flush against the fiberglass, if there is enough surge to push the rail and the side of the boat in together, either the fiberglass will push the soft aluminum back out but still looking uniform with the side of the boat, or.. it wont. and then it will be a bit more than a new aluminum rubrail
reason 4 is... like anything else, the rail has to have a firm foundation for longevity.... put the rubber on the outside if you need a spongy bumper effect.