You raise some good points.
With respect to the HRI Ultra-Thin crust pizzas, I have never read anything about how they are made in HRI's frozen pizza plants. However, while some thin-crust pizzas, like cracker-style crusts, can be laminated (member fazzari of this forum is an expert on this approach), it isn't absolutely necessary to get what appears to be a laminated, flaky crust. However, to get the flaky characteristic in an Ultra-Thin type of product, it definitely helps to have the skin very thin (for example, a thickness factor of around 0.05-0.07) and to pre-bake or par-bake the skin. Docking the skin is also often a good idea. These steps seem consistent and compatible with HRI's methods used in its frozen pizza plants. Like you, I am inclined to believe that the same dough is used for the thin crusted pizzas as the basic ones.
I believe I was the one who commented on the paucity of sauce on the HRI pizzas that I dismembered. However, in actual practice, I am sure that more sauce is used than what I measured. What I measured reflected a loss of water during baking. Typically, a pizza sauce has around 88-92% water. However, not all of the water is lost during baking. Unfortunately, there is no good way to calculate the weight loss of sauce on a pizza, and especially one that has undergone some baking before it is in the hands of the consumer. There are also weight losses for the mozzarella cheese (a low moisture part-skim mozzarella cheese is around 46-48% water) and in the dough. Since it is difficult to assess these losses, the approach I take is to make an estimate of the extent of those losses and factor them into the quantities of ingredients used to make the unbaked clone. For example, for a basic HRI frozen pizza, like a plain cheese pizza, or a pepperoni or sausage pizza, I would use something like 10% as a loss percentage.
I also agree with you on the need to bake the pizza long enough and at the right oven temperature to get the crust to simulate a frozen HRI crust. In my case, by completely defrosting the HRI frozen pizzas to conduct tests on them, I no doubt changed the thermodynamics of the pizzas and also the bake times. However, based on my limited experience with an HRI type of dough, specifically, in a home clone setting, I would suggest that the skin be docked and pre-baked for several minutes, maybe three minutes on a dark anodized perforated disk or cutter pan, at around 475-490 degrees F, before dressing and baking it. In its frozen pizza plants, HRI reportedly uses a 90-second pre-bake. That is for a crust without a carrier. That might work in HRI's conveyor ovens but I do not think that that is long enough in a typical home oven, especially if a carrier is used. Since ovens vary by type and from one brand to another, this is something that will usually require some experimentation to achieve the desired end results. The advantage of the pre-bake or par-bake is that it allows one to use more toppings without turning the pizza crust soft. The impression I have gotten from my reading is that the HRI pizzas from one of its pizzerias have a more tender crust than the frozen ones.