What I know, which is basically what I've read here on TB.net, would confirm your concerns about using silicone on your alum boat.
Acidic vs neutral? I'm going to go out on a limb and say acidic silicones would not be a good choice on our alum boats. I'm not sure of your specific application but there are a whole bunch of products available that I see discussed in the Boat House and Modifications forums. For all I know some of them may be silicone based. I would sure read the label for compatibility for using it though.
Sorry I can't be of more help.