I have the issue - even after all calibration with the vision encoder as well, the holes are .1 to .3 mm smaller than they are designed. With my P1s, the sizes are 0.005mm off. I use on both printers the same spool of Bambulab Basic PLA.
I could try the hole compensation, but it seems not the right solution if all my other printers do not have this issue.
Does anyone has an idea or is it a bug?
With your P1S the sizes are only off by .005?? Are you sure you wrote that correctly? Maybe you mean .05? Which is really good accuracy for a 3d printer. .005 would be insanely good accuracy. My P1S is accurate to .1mm. When I make a 6x3mm hole for a magnet I have to make it 6.15x3.1. Although I haven’t tested my H2D, judging by the even better prints alone it must be as accurate or better.
For an average printer I’d say .1 to .3 was pretty good but it is not good for the H2D especially with the vision encoder and its claims. I don’t know what could be wrong but you may find it helpful to look under the shrinkage settings. I have never played with those settings but maybe someone else could chime in to help.
Hahaha, yea 5 microns, measured with what, a ten dollar caliper 
Anyway, yea compensation is often required machine to machine.