Keel bolts
I think you answered yourself!If water is in fact seeping from a keel to hull joint separation up into the bolt holes, sealing the holes only from the bilge side may indeed keep water out of your bilge, but it won't prevent sea water from sitting against the bolts within the bolt-holes, and, as we all know, stainless steel eventually rusts just as well as anything else exposed to sea water!For a proper job, I would take the boat out of the water, loosen the nuts a bit, throw some "Salt-Away" in there and let in seep into the bolt holes, rinse, let dry thoroughly, and then seal around the keel if that is where you eventually spot some separation.