With the passage of time, things change. The ingredients needed and available to make the pizzas change, the suppliers and pricing change, the equipment used to make the pizzas changes, management personnel changes, and workers who make the dough and pizzas come and go. The laws and regulations that govern the business change. And the economy can change, for the better or worse. But, throughout all this, the basic dough recipe can be the same. In theory, you might be able to replicate a pizza of years ago, for example, such as was made by Buddy's when they used deck ovens, but that pizza will not be the same as one made after they went to conveyor ovens, both infrared and air impingement conveyor ovens. We also should consider that workers don't always do things "by the book". They improvise where necessary, they make mid-course corrections, and I am sure that sometimes they are indifferent and just "wing it". I think that is why pizzas rarely look alike, even in the same store.
In your case, your objective should be to make the best pizza possible that you can sell at market at a reasonable profit, and do it consistently. The Buddy's clone dough that you are now using, with a one-day cold fermentation, is already different than the dough that Buddy's uses, which is the emergency dough. It may also well be that you are using a higher hydration than Buddy's uses, and maybe that is responsible for the taller crusts that your pizzas have. If so, you are essentially selling customers more air, which can create the appearance of greater substance. I could be wrong on this but given a choice between a thin, more dense crust and a thicker, more airy crust, I would think that on balance your customers would prefer the thicker, more airy crust.
Maybe one day we will find out what weight of dough balls Buddy's uses for its pizzas and the hydration value for those dough balls, and maybe even how they make their dough, but that shouldn't change what you are trying to do. Each of the old timers, and even many of the current players, who started out with essentially the same dough recipe went on to place their own creative signature marks on their pizzas to differentiate them from their competitors. I suspect that you will end up doing the same.