Holding a 0.0001" tolerance is pretty easy if you don't rush. (one then thousandth of inch)
I used to teach people how to do it in a couple of hours.
The 'trick' is knowing what to do if cylinder is tapered or out of round after boring (or even worse, tapered and out of round)
As cylinders heat up while being machined, slight taper is pretty normal
Major problem with real tight piston/cylinder clearance is the possibility of 'cold seizure' where piston expands faster than cylinder (ADC knows it's common with wannabee's on HD's, look Ma, revving it to warm up faster)
I run my 378 motors with 0.0016~0.0017" clearance.