Well, using a pair of calipers isn't the best idea. When flattening a stone it's pretty hard to put equal pressure on all corners, and so to have the stone vary in thickness on one corner or the other by .005" would be a hard thing to avoid. Measuring the actual flatness of the surface in that way just isn't possible; at least not in a very accurate way. Aside from all of this, let's say for example you have a big low spot in the center of your stone, your calipers will probably take readings from the high-spots surrounding it before ever hitting upon the low spot, and then if one corner of the stone is .005" thicker than the other, it just compounds things.
I don't know how flat glass is, but I would assume that the standard practice of rubbing a stone on sand-paper fixed on glass would probably give you a surface flatness of about +/- .001 - .002, because the paper itself will probably vary in thickness in terms of the distribution of abrasive, adhesive, and of course the paper itself.
DMT stones are flattened to within +/- .001 though, and I think that flattening on this surface should get you to +/- .001, which in my opinion is all one would really need. Most surface plates machinist's use are only accurate to +/- .0005, so .001 is nothing to scoff at. You can pretty much create a vacuum seal between two surfaces when you talk about that kind of flatness.
Finding an accurate way to actually determine that you've eliminated all the high and low spots and have flattened is the only real way to do it. That's why I would use the pencil-grid trick, or maybe a few light dashes of some magic marker once it's mostly flat since the slurry produced by flattening a stone tends to erase the pencil and can lead to a false reading of flatness. Marking a grid like so will leave the markings on the low spots, and once the markings rub away, then you know the surface is flat; at this point you could still get some wild variations with your calipers if you tried to measure it based on the thickness of the stone.
Realistically though, any flat surface like glass with some sandpaper on top will get the stone very flat. I've used laminate counter-tops as the backing underneath sandpaper, and they work very well. A good way that I've used to test if a surface is good for flattening, is to take a machinists' square and a small flash-light. Put the square on the surface, and the flash-light behind it. If you can see a crack of light shining in underneath the square, then it's probably not a good surface to use.