To prep the aluminum for painting, use DX533 and DX503 products from PPG
DX 533 is a phosphoric acid based cleaner and DX503 is chromic acid based conditioner that will form a chrome conversion layer on aluminum. DX503 Is the equivalent of the Alodine brand name from Henkel Technologies. If you can find the Alodin easy, use it. I just could not find at all near by. PPG product are carried by most autobody supply stores like Wesco.
Evaluate the boat for any possible galvanic corrosion near this area before you make assumption that the silicon was the reason for the pitting. Look for things like a rivet that was changed in this area, Maybe it is not the correct material; or a penny that fell down on the hull from someone's pocket