I disagree, mellorp.

Basic problem of any manufacturing process is that you cannot avoid certain tolerances. There are tolerances caused by systematic effects as well as random effects.
Honda specifies a very small piston-to-cylinder gap. This is only possible if you classify the machined partscylinders and pistons and then use combinations that deliver the small gap you want.
I am sure that re. machining precision not a lot has changed within the last 20 years. Less precision and selecting combinations is cheaper in the end.

Piston/cylinder - which is matched to which?
You can't match a piston to a cylinder. Pistons are oval, tapered and who knows what else. A cylinder is 100% round and cylindrical.The old plating is removed, bore measured, thickness of new plating minus honing is considered and matched to one of the available piston sizes.