Firstly, I've found over the years about 1/2 of what you read on Bob's is good info, and the other half of it is garbage. Whether it's intentional misinformation, I'm not sure. As for setting the top ring end gap to .004", IMO that one is garbage. I think you want at least .004" per inch of bore.
As for why the the ring and the cylinder, while made of similar materials, don't expand the same: It's a surface area to volume thing resulting in a different
rate of expansion.
Let me explain.
Surface area is to the 2nd power or square, and volume is to the 3rd power or cube. As an object gets very small, it's surface area and its volume become closer to a 1:1 ratio. As an object gets larger, this changes rapidly. See link below, also see table.
https://en.wikipedia.org/wiki/Surface-area-to-volume_ratio
The above table is for a cube, and our shapes are different but the same principle applies.
The point here is because the ring is much smaller than the cylinder bore, the ratio of surface area to its volume is smaller. This results it the ring heating more rapidly than the cylinder, and therefore expands at a much faster
rate.
It is the rate of change in temperature and the resulting expansion that is the reason they don't achieve their final dimensions at the same
time. Cold seizure in a two stroke is
a perfect example of this. Or think of two parts of aluminum, equal in volume (for this example weight). One is .062" thick sheet metal, the other is a small billet cube. The size and surface areas of the two parts are completely different but the volume (weight) is the same. You expose both shapes to the same torch for the same amount of time, which heats faster?
We could also discuss the opportunity each part has to cool, and the eventual equilibrium of an engine running in steady state in terms of heat loading of the different parts and heat flow out of them. The ring relies on its physical contact with the cylinder and piston to transfer heat. The cast iron cylinder relies on its contact with the aluminum block and the air-flow over the block to transfer its heat. But that's more than I care to type.
I probably did a crummy job of explain this....but I hope you can understand what I'm talking about.