The stability and precision of your positioning setup is very important, if it moves/flexes by any amount, that’s the XY error you’ll get. I had problems with claws biting into material, that alone can easily cause a 0.25mm error. Hence the gauge blocks, which helped a lot.
For Z I think your approach is just fine, and the approach with a piece of paper should work just as well, I just happen to use one of the gauge blocks as a replacement for a piece of paper 
See this discussion: Actual size of the #102 endmill (where kind people were also quick to point out that I should never ever try to measure and endmill with calipers!).
I started doing test cuts with endmills just to verify what I’m getting and the results were… surprising. Some of my most precise endmills turned out to be from Aliexpress (Dreanique brand). The #102 I got from C3D with my Nomad is way off and I don’t use it anymore. It won’t be off by 0.1mm, but -0.05mm is fair game.
But, the biggest source of XY error for me after fixing my workholding setup was deflection when going too fast (climb milling) while cutting the outer two reference walls.