From a chemistry perspective, you're right on the money. In theory, the siloxane group of a silicone polymer can form a bond with the hydroxyl group on the methacrylate polymer. In practice, it seems that this isn't a very strong bond, and is far weaker than the siloxane-silicon-dioxide bond formed with glass.
Epoxy is quite different, and appropriately cleaned acrylic surfaces will bond incredibly securely with an appropriately cleaned glass surface using this compound. I glue my overflows with epoxy for this reason - not sure why very few others do.