Ah-ha, now things are becoming clearer.
It appears that the "rails" have mounting bases that are sitting on top of the "gunnel" you speak of, with the stainless bolts passing thru the gunnel with washers/nuts underneath.
Yes, that situation is a good candidate for using the butyl tape under the rail mounting pads, (and under the washers).
You'll want to clean-up the bubbled paint/bare spots and coat with something, (I'm not sure just what for a "good enough" job).
Then you can re-install the bolts with one of the products that others have already recommended, (I do agree that Tef-Gel isn't the best for that application), something that has some "body" to it is better.
Those mounting pads were probably trapping
water underneath them.
The
water eventually goes away and leaves the
salt behind to
work its evil deeds.