You obviously haven't checked, squish, or port timing in a number of engines, or know how manufacturing goes. The fact is mass production parts have a set tolerance they have to meet. Sometimes the tolerances are at one the end of the spectrum, sometimes, the other end, and sometimes they're spot on. Cylinders, pistons and cases are rough castings, to get them finished, and within speck, they have to be machined. Sometimes these parts have to be machined to the far end of what's acceptable to prevent waste. This is what happens in mass production.
Now, if you were building an F1 engine or Nascar engine, this would not occur, those parts are discarded. These are chainsaws the tolerances are quite crude honestly. Some manufacturers have different tolerances allowed, check the radial crank runout on a Honda VS a Harley-Davidson.