Anyway, I hope some of the above helps.
Thank you for your thoughtful post.
The idea for the thickness factor came from Tom Lehmann, of the American Institute of Baking. However, he usually refers to the thickness factor as a "loading factor". I took Tom's idea a couple steps further from what he was doing by combining the thickness factor in the various dough calculating tools with baker's percents and the bowl residue compensation factor. That added a lot of versatility to the dough calculating tools. The bowl residue compensation factor was not my idea either. I took that from member Jeff Varasano's website when he was making pizzas at home (he is now the owner of the eponymous Varasano's in Atlanta, GA).
Toward the end of last year, I updated my list of typical thickness factors for different types of pizzas at Reply 1 at http://www.pizzamaking.com/forum/index.php/topic,12243.msg115759/topicseen.html#msg115759
. Some time before that, through an email exchange with Tom Lehmann, I calculated a thickness factor for his NY style dough formulation of 0.0882813. I started out higher than that and, as a result, became attached to the higher value. But one of the values of the dough calculating tools is that you can pick whatever thickness factor value you prefer.
FYI, the thickness/loading factor can also be used to extrapolate the amounts of sauces, cheeses and perhaps some toppings from one pizza size to another, much as Tom Lehmann has used that factor to extrapolate from one dough batch size to another to make larger or smaller pizzas. Tom discusses how to do this for cheese and sauce in one of his PMQ Think Tank posts at http://thinktank.pmq.com/viewtopic.php?f=6&t=6169&p=38621&hilit=#p38621
. I have used that approach many times for sauce and cheese to be sure that the larger or smaller size pizzas have the same characteristics as the pizza from which I did the extrapolation. It is also a good approach for professional pizza operators to use when they offer different size pizzas. In fact, many such operators have found that they were using too much cheese on some pizzas and were able to save quite a bit of money by using the loading factor approach.
As a bread baker, you will perhaps be interested to know, if you haven't already discovered it yourself, that the preferment dough calculating tool can also be used to come up with dough formulations for naturally-leavened bread dough. However, the ingredients for the preferment dough calculating tool are limited to flour, water, yeast (three types in addition to the wild yeast), salt (4 types), sugar and oil. You would use the Dough Weight option in the tool since thickness factor does not apply to bread dough (unless, I suppose, you are making flatbreads).
You are also correct that the preferment dough calculating tool uses a different "hydration" methodology for the preferment. My recollection is that Mike (Boy Hits Can) and I concluded that it was easier to program the tool using the alternative hydration calculation, but to avoid confusion as much as possible we put the following statement in the box where the data relating to the preferment would be entered: Note: Preferment's percent of water = (weight of water divided by total weight of preferment) x 100.
When I first started experimenting with natural preferment versions of the basic Lehmann NY style dough formulation, the various dough calculating tools did not exist, and my understanding of preferments, both natural and commercially-leavened, was quite rudimentary. However, I came to understand the math involved and, with Mike's help on the programming side, we were able to create the dough calculating tools that embodied what we learned. The preferment dough calculating tool was one of the hardest to devise, along with the deep-dish dough calculating tool that had some messy math that we had to program into that tool. But all of the dough calculating tools are unique, one-of-a-kind tools (as best I can tell) and quite useful to our members. I consider them and my digital scale to be the two most useful things I have to make pizza dough.