I was out of town again when you entered your last few posts, but I am back home again and have reviewed this thread again to get me back up to speed.
I agree that the inside crust of a Zachary's pizza is likely to be thinner than what you have been testing, based on the fact that the inside skin used to make a Zachary's pizza overlaps the deep-dish pan so much. I am also now suspicious of the 2/3-1/3 ratio. Had the original recipe given actual weights for the two dough balls (one for the inside crust and the second for the top thin crust), we would have a better grasp of the numbers. I think the Zachary's folks who came up with the recipe just guessed on the ratio to simplify matters for home pizza makers who might attempt the pizza.
I also am inclined to believe that the hydration of the Zachary's dough is properly on the low side. That, coupled with the small amount of oil used in the dough and rolling out the dough for the inside skin so that it can overlap the pan by such a large amount, should yield a fairly crackery crust with what appears to be layers and with crumbly characteristics. Such a crust shouldn't be crispy, only cracker-like but with some give without completely breaking. For a Zachary's-like inside crust, I think you might want to use a thickness factor of around 0.095-0.10 as a test value. The top thin crust might have a thickness value of around 0.05-0.06, again for test purposes.
With respect to the flour, you might consider using General Mills' Better for Bread flour. That is a softer flour than other bread flours and might be suitable as a substitute for the Ceresota/Hecker's flour that many deep-dish operators in the Chicago area use. The Better for Bread flour is also an unbleached, unbromated flour (as is the Ceresota/Hecker's flour) and, as such, should pass muster under California law. Another flour possibility is the Pillsbury bread flour. If I can find specs for the Better for Bread and Pillsbury bread flours, and then compare them with the specs for the Ceresota/Hecker's flour, maybe I can zero in better on which flour is the better one to use.
Until we see if you can get closer to a Zachary's clone pizza, I am inclined to stick with the baker's percents that we originally came up with from the recipe you posted. If you can tell me what size Zachary's clone pizza you would like to try next, maybe we can come up with a test dough formulation for you to use. Of course, any additional information on the Zachary's pizzas that you can come up with is likely to be helpful. In this regard, I was glad to hear that you were able to confirm my suspicions that Zachary's is using roller equipment (hand rolling with Zachary's volume of hundreds of pizzas a day just wouldn't make sense). If I had to guess, I would say they are using either an Anets or Somerset dual-pass roller.