I can understand your confusion. There is something complicated going on here, so let me try to explain it.
I’m going to distinguish between the “design” and the “process” used for building a chip. Let’s say my simple circuit is an inverter: A = NOT (B). In CMOS (a popular flavor of transistor types, if you will), you can make that with two transistors and some connecting metal. How I connect those transistors, the length of the metal trace, the width of the active gate of the transistor, and so forth, are all part of the design. (I am only slightly oversimplifying for illustration.)
But this design has to get built using a manufacturing process. For the transistors themselves, some machine has to spit ions of some impurity (like Boron or Phosphorus) into the silicon where the transistor goes. It has to be set to give a precise amount of these impurities. For the connecting metal, it is deposited to a certain thickness, and then etched to a certain thickness. Etching can also reduce – or not reduce – the width from the design portion.
Right away you should notice that the manufacturing process – the thickness of the metal, the doping of the transistor (which relates to it’s electrical characteristics, like maximum current, leakage current, turn-on voltage), and so forth – can be varied independently of the design. That is to say, I take the same design, and on Monday I set the dials one way and make one batch, and on Tuesday I set the dials another way and make a different batch.
Now, the speed of this design relies fundamentally on the resistance, capacitance, and inductance of these circuit elements. These characteristics, in turn, rely both on design elements (transistor drawn width, drawn metal size) and process elements (actual widths, metal thickness, impurity doping). That is why taking the same design and varying the process results in different speeds of the units. (It can also change other things, like power consumption, and reliability.)
What’s worse is that with the top technology processes, all of these parameters are so sensitive to change that they cannot be controlled precisely. There is some natural variation that is going to occur, and you can’t help that. What you can do is make your design robust enough to withstand as much variation as you can; control your process to have as little variation as you can; and set your center “goal” for each step of your process so that the natural variation is firmly within what the design can tolerate.
Within that variation, of course, are faster and slower chips. You go and test them afterwards, everything that is 100 RSU’s (random speed units) goes in this bucket and we charge $ for them, and everything that passes 150 RSU’s goes in this much nicer bucket, and we charge $$$ for them (for there are fewer of them, but more people want them). THAT is the production issue.