the usual methods I've heard of involve using a strip of paint soaked cloth as a gasket between wood parts that are screwed together. the pieces are assembled with the paint is wet, and the screws are tightend enough to squeeze a bit of paint out of the gasketing material. When going over heavy canvas skins, frequently a layer of paint on the skin was sufficient, and the keel or other parts could be screwed down.

Since your skin is so thin, and already coated, you might try adding a strip of dacron an inch or 2 wide down the keel. You have a seam there? Fine. Glue the strip over it with a couple coats of whatever waterproofing coating you are using, and then screw on the keel to hold things in place. If the coating glues down the edges fo the fabric smoothly, leave them alone. If the edges don't stick down, trim them even with the sides of the keel by using a seam ripper (a tool most seamstresses know). Go slowly and carefully to avoid cutting into the hull fabric.

Your idea of using a silicone sealant is a more modern approach. It should work well. If that is not handy, you might try a couple coats of rubber cement (from the stationery department).

PGJ