I think that’s a really neat idea.
I was thinking in a slightly different direction. Suppose you have a thick rectangular aluminum plate of known dimensions (or a block with aluminum tape on all sides or something which you measure with callipers). You put it on your spoil board and touch off at various points along all four sides (with a wire to the plate and another wire attached to your end mill). These measurements would allow you to find the perfect skew correction. It compensates for frame and gantry skew at the same time.
A different variation I thought about is inspired by the heated bed and PINDA probe of the Prusa i3. To measure skew, the probe finds the center of screws (or other metal, not sure) in the heated bed at known locations. It makes several passes over each know location and find the highest point which triggers the probe. This is a standard feature of the i3 firmware, but I have no idea how it works in terms of gcode etc.
You might be able to screw some round-head screws into you spoil board and use a Z probe with the same procedure. You would need to know the location of those screws very accurately though. The i3 solves that by using a PCB as the heated bed, which can be fabricated very accurately.
It’s an interesting rabbit hole to go down, but I’m not sure if I’m willing to go much deeper 
I’ll first get a bit more hands-on experience with my MPCNC.