Nice setup going on there. You could use a foam underneath it if you really want. Does the glass sit flat? Or is it on a plastic rim? If it is flat, then neoprene or some type of foam directly across the whole tank works fine. If it has a trim then only foam the trim part.
I honestly don't think you should have to foam any of it. If I recall, granite is pretty dang straight and should not cause an issue. I've never seen a warped piece of granite.
I agree with the total water volume also. If it's part of the system, then add it in. I'd possibly add a internal pump into the cistern that you can turn on that would churn the whole thing up very hard to get any excess nutrients.