And, you have found my only complaint about the RPi, no mounting holes. On the plus side, I have some toughts on getting around this.
Thought 1: I have seen nylon standoffs that are side-clip, instead of top screw. A couple of those with some mounting holes in the base would have you set up pretty good. (I remember seeing them on Adafruit, though I can't find them now. You might PM LadyAda about them)
Thought 2: Since this is a milled case, design in a couple of ledges around the outside, on both the top and bottom. The ledges can hold the board in place. (let me know if you're having trouble visualizing it, I can do some quick and dirty drawings, if needed)
I'm only wearing black until they find something darker.