I keep asking my self why the designers ever thought this was a good way to build this connection, seems like it is destined to fail at some point.
After studying the pictures more throughly, I'm somewhat inclined to agree with you. The hull construction at the crossbar endcaps is quite complex and yet the connection is really not that good. The fact that the prongs on the endcap largely bear against foam is disconcerting. Plus the fact that any water that leaks past those prongs will enter direcly into the foam core of the fiberglass sandwich is not good. Also, the screws for the end cap only grab onto maybe 1/8" thick fiberglass and again, you have a direct leak path for water into the hull structure.
One thought that comes to mind for repair would be to remove the foam from inside the hump and fill with epoxy as you're talking about doing. But also bond a threaded stud (or studs) into the endcap. Then drill an additional hole in the aluminum end cap and tighten the end cap against the hump with a nyloc nut and washer. This would hold the end cap against the hump better than the self tapping screws that are already there. It's very common for those screws to loosen, and when they do, the end cap wiggles and wears out the prong holes causing the boat to get sloppy.