In the case of Honda's engines: Sochiro blazed a new path in motorcycle piston design, and became famous for it during the 1960s. It came from his experience with making piston rings for cars before he made bikes, I imagine...
All of these bikes use 0.0008" to 0.0012" clearance on the pistons, regardless of bore. The pistons he had ART make for him included a surface finish that is slightly porous to a depth of about 0.0004"/0.01mm, which holds oil readily and burnishes the skirts to a high sheen in about 500 miles (if the oil is good). This was a cheap method of something better that he did in Honda Racing. Starting in the 1990s sometime, this porous method was augmented with the alternate racing one: today's higher-quality pistons come with micro-grooved skirts of about 0.0002" depth. These function similarly to the porous surfaces, and also allow for bore-matching a little faster. Typical break-in time is about 150 miles on these. The pistons from Z1 Enterprises and Wiesco, among others, show this method. It appears to now be done with CNC machining: the racing pistons of the 1960s had it done by hand and it wasn't always so perfectly even...
In my experience, the engines that perform best and last longest, running cooler and never using oil, are the ones that started out at 0.0008" clearance. I know of some roadracers who went tighter, at 0.0005", when the cams had more duration and overlap: since they don't see a lot of face loading at low RPM (due to the cams involved) they also don't warp from the pressures: those bikes had no trouble exceeding 14,000 RPM. [Successful] Four bikes used in drag racing, with 900cc and 1000cc pistons and shorter duration cams (for more launch torque) used up to 0.0015" clearances with gas-ported top rings to improve the sealing and heat ransfer into the pistons.
As these engines age and the skirt-to-bore clearance gets bigger, the pistons run hotter because the contact (through the oil) to the cylinders gets less effective. At first, this extra heat swells the piston a little more, making up the difference: after a while (typically at about 0.0020" or more) the pistons don't swell enough to transfer as much heat as they should, and they strat to get too hot. This causes the rings to expand too much, which wears them and the bore more, and their gaps soon grow. This lets oil by, which washes the sides of the pistons unevenly (carbon removal), and the pistons tilt: this action causes even less heat transfer and the system soon fails. This usually occurs at about 0.0030" of clearance or so.
Honda's manuals show 0.0032" as the maximum clearance they allow in this area, but what few folks seem to remember is that this means, "...with cleaned pistons and bores, and only this much clearance in one place of the bore". Since the bores always wear in an uneven oblong shape (as viewed from above or below) with the largest clearance toward the coolest portion of the hole, this is always one spot in a bore. For example, the front outside quadrant of the outer bores, and the middle of the two center ones (toward the camchain tunnel) always show the most gap in a carefully measured hole with lots of miles on it. Even at this clearance, honing and installing new rings gives just about 10,000 miles before oil becomes uncontrollable, and the performance is way down from normal to boot.
