I just squared my spindle using a combination of both methods (pushing up with the Z axis with both rails loose & shims – altho I used plastic from some packaging).
To measure how far off square I was, I used the following contraption, made from a dial indicator, some 1/4" rod and some scraps of plywood.
I got the side to side height difference to less than a thousandth (over 5" distance) and the back to front to less than ten. When I milled my work surface flat, I used a 1/2" bit and you can barely feel some texture to the MDF. I think it will be fine with the more usual 1/4" or 1/8" bits.