The Great Stuff Foam is made to resist water and stop leaks in cracks and is the same product used to build outdoor water falls. The silicone does seal the GS to make a better waterproof barrier but is also how we attached the substrate for a natural covering.
If your looking to seal the plywood which needs to be 100 percent separated from the moisture getting to it, there are paints which will do this as will the regular GE II silicone. I'm not positive the paint but there are a few construction journals that I thought someone posted using, like SludgeMonkeys.
Hopefully someone will pipe in with what is best for sealing off the plywood.