My thoughts are that if you print in ABS and the result was what you showed in the images, all should be fine.
ABS requires higher temps to build so there is more shrinkage then PLA.
If your prints are with PLA, you may see if you could tweak it a little. But to be honest I think your prints are fine
and the more you worry about getting your prints 100% accurate the longer it will be getting your MPCNC up and running.
I’m printing with a Devinci 1.0A and I’m unable to calibrate, apart from the first layer and bed height. Which can be a pain
in the butt at times. But the print you showed is very similar to what I would get on mine, and my MPCNC is fine, with a bit
of hand machining!
Good luck with it all Gianluca.