I had the same issue except mine was a small hole at the same location you describe.
I used GOOP brand adhesive (the marine version). Works like a charm. When you dispense the product it settles down near the surface of the top; kind of like self-leveling. Don't touch it, just let it settle.
It is rather shiny so it's noticable on the top but since the alpine bar is up so high, you can't see it. No leaks and this was done two years ago.