*Sniff Sniff* this is the first time someone specifically asked me a question on the forum. **gets misty eyed** I'm touched!
Yeah okay so I put building foam under acrylic tanks but not glass.
Let me put it to you this way... All fish tanks are designed to sit as provided on the hypothetical "perfectly flat surface." If the braces are there under the tank, they are there for a reason, so no, you don't remove them.
Acrylic is more flexible than glass so generally acrylic tanks with flat bottoms need more continuous support along their entire bottom surface.
All of my glass tanks sit directly on the stand, but I design stands to provide this flat surface. When I build a stand, I design it so the tank sits on either a face frame or directly on the stand's structural frame (2x4s, 2x6s, etc). In either case, I run these items through a table saw or a jointer to make them perfectly true and flat, so there is no need for foam in those cases.
If the tank and stand you obtained were from the same source and were previously used together, I'd tend to think you could continue using them just as is without any problems. As Acrylic stated, you're dealing with warranty issues here. Foam is really something that is either specified by the manufacturer or is used when custom building stands. When you are using a DIY stand, the warranty is voided anyway.
As for your rock, there are two schools of thought on this. Zman makes a good point. The sand will serve to spread out the load and prevent the rock from exerting a lot of weight on a very small spot, something that can easily shatter glass. The other school of thought is to place it on the glass and fill in the sand around that. The thinking here is that it will keep burrowing animals from causing a rock collapse, and will prevent detritus accumulation.
I have a good compromise, but I will confess I've not tried it yet.
Lay eggcrate across your entire tank bottom, put in sand to just fill the squares of the eggcrate, then put the rock in, then the rest of the sand. The eggcrate will discourage burrowing too deep, will help to keep the rocks steady (the 'compartments' will grab little points of the rock and keep it from sliding), and will help to distribute the weight.