I'm getting to the limits of my understanding here, I'm not an engine builder, but have built a few and had a few race engines built for me, I even had to custom design some pistons when an engineering shop planed a block when I had told them not to.
I believe that pistons are not round when cold because you want them to be round when running and up to temperature and the material is not evenly distributed, largely because of the gudgeon pin. So they are cast / forged allowing for the differential expansion. Similarly the top of a piston is hotter that the lower area so the dimension above the first ring tends to be smaller - to a greater extent on turbocharged engines.
Bores are round when new, but, perhaps to a greater extent in boxer engines, they tend to wear oval.
I think it's best to simply measure where the manufacturer advises. They know where the measurements are being taken and what the wear limits when comparing those measuring points. If you are taking measurements at different points, the basis for the clearance calculation has changed so is the resulting answer of value ? It' a bit like measuring in inches or cm. Both function well as measures of distance, but you need to know which one to use at any point in time, (otherwise your Mars lander crashes)
![Embarassed :oops:](./images/smilies/icon_redface.gif)