Either way, it's to be expected that the smallest iPhone 12 is going to offer the least performance. It's going to have smaller galvanic cell. Meaning it won't be able to provide as much current to the chip (= less power, lower frequencies, less performance). There is going to be less space for any kind of heat spreading device. And the surface area of the body is smaller, which means lower cooling capacity for the same surface temperature (even if you could get the power, the chip would be running hotter - that is if it didn't throttle). Even with identical chips, you can expect smaller devices to be slower and larger devices to be faster.
As for actually making a different chip, you have to remember economics of scale. Chips are very, very expensive to design. Apple actually uses fairly large chunks of silicon so their chips are relatively expensive to manufacture, but the actual cost of making more chips is significantly lower than what would be the sticker price. That's why Apple can put their latest, most powerful chip into an entry level (for their brand) device. The design is already paid off and the manufacturing line is ready and has free capacity (the cheaper devices come when the demand for the more expensive devices has died down). It also makes for simple logistics. I'm not expecting the mini to be the best selling iPhone 12. Even when you add the future SE into the mix, I'm not sure there is enough volume to justify it. Obviously, it would depend on the exact change.