It seems weird to bump this thread, but this project is not dead in the water. i just put it on hold for now with my 12L scratch build taking priority.
When I get around to it, I will just throw in a different sort of build, a budget Hackintosh that can do some light gaming, because I miss having a Hackintosh since the days of owning a Intel Bad Axe mobo. Parts bought shouldn't exceed $250, so yea it's really budget 
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Now I'm getting around to thinking up how to design the inner frame, and in particular the motherboard tray. I can't use PEM fastener standoffs as I don't have access to the tools to install them, and regular screw-in hex standoffs will protrude too much from the bottom, so I'm thinking of clever workarounds.
Then I noticed my unused Dell Optiplex SFF case has standoffs that are punched in/pressed in from a sheet metal base, like this:
They are cone-shaped elevations that are part of the whole sheet, so all you need are the screws to hold the motherboard in.
I'm thinking of taking the concept with bent aluminum sheet. But I can't punch or press indents on the sheet here, so it will be something similar in design. What if I took a sheet and did 45 degree bends around the holes to raise the level above the bottom of the case?
Here's a cross section view of what I'm thinking of:
So the "standoffs" are the raised areas from the diagonal bends. These areas will only touch the very close area round the holes. There will be a large cutout on the middle so it's not like the bumps will touch length-wise across the whole motherboard. I don't know if anyone here has done that with their cases but it seems to work fine with a lot of OEM cases in steel, and aluminum might be able to hold just about as well.
