I have a standard-size SO3 but that isn't going to stop me from making some observations.
I arrived at this point at about the same time as I noticed this thread. I've replaced the stock spoil board (the previous owner had chewed it up pretty good) and then I wanted to add a second 1/2" board on top of that, so I can clear the front and rear brackets of the SO3 (so I can use longer pieces).
I wanted to make sure my board was fairly flat relative to the Z so I made a DI holder that goes where my dust boot would normally mount.
When I purchased my SO3 (used), I noted that there were no feet on the bottom of the unit. Having the unit sit on my workbench, I didn't want the waste/spoil board screws that were protruding from scratching-up my bench top.
So I visited my local Ace hardware store and purchased some vinyl bumpers. They're 3/4" square and 1/2" high. I placed nine of them on the bottom of the SO3. I had figured these bumpers would be made from hard enough vinyl/rubber that they would not compress.
Checking w/ the DI, I think I can compress them by about .004 or .005" by applying pressure to the spoil board with my thumb. It is also possible my bench itself is moving that much. Could be a combination of the two, as well.
In testing various areas of the spoil board, I'm about +/- .003 or .004" across almost all of it, save for the front left corner which I think is about -.009.
My intent all along was to shim under the feet of the SO3, or under the corners of my top spoil board, to get everything to +/- .003" or better.
Before proceeding, though, I think I will replace the bumpers with some discs I'll cut from plywood, so I can remove the compression of the bumper from the equation.
The thing is, if you guys are setting your entire machines on top of foam rubber padding, it doesn't surprise me you can get quite a bit of movement.in your spoil boards. I assume with those larger units you're using foam to deaden sound coming from the larger panel, sort of acting like a drum head?
If that is the case, the solution may be to use some panel damping stuff normally used in cars and speakers to reduce noise, while also using some sort of solid/hard feet that can accommodate shimming. So the SO3 ultimately sits on hard feet.
Or I may have completely misread the problem in which case, never mind.
FWIW, the DI shows quite a bit of action ( a few thousandths is easy to achieve) when pushing the Z-carriage to and fro. And I can push the rails and get .001 or .002". My point being, if I'm going to start quoting machining jobs for NASA (kidding), I'm going to need to fix any variability I can actually fix.