It has taken us 19 pages and 374 posts to get this far, but overall I think we have done a creditable job, or got lucky, in being able to at least get the physical characteristics essentially right--including weight, crust thickness (including thickness factor), size and flexibility. Moreover, you did not have to do endless experiments. And each experiment taught us something new and useful and valuable. I think what helped us a great deal is having real Ultra-Thin crusts to examine, play around with and to compare with your results. I think also that the use of the two cutter pans and baking the crusts only to the point of the starches/protein gelatinizing was a lucky stroke that saved us a lot of time and effort.
As I see it, the main missing link at this point is the types and brands of flours used by Ultra-Thin. However, as I have discovered before with other reverse-engineering/cloning exercises, there seems to be a fair amount of give and take in the amounts of ingredients used without showing up in the final product. It would be nice to try using a lower protein flour, like a bromated bleached bread flour, along with a white whole wheat flour, if only to try to be more faithful to the Ultra-Thin ingredients and quantities, but I believe that it should be possible to balance the amounts of the Kyrol flour and the KA regular whole wheat flour to get comparable results. We may learn differently when you try making a pizza from the latest crust and have an opportunity to test the crust for flavor, taste (like or don't like), color, aroma and texture (e.g., soft, chewy, crispy, cracker-like, or some combination).
On the matter of the dough coloration, one thing you might try is brushing the dough with a bit of oil before going into the proofing box. You might recall from the many patents we read that is was a common step to oil the dough balls as they were proofing and before forming into skins. Since that surface oil will usually migrate into the dough, it perhaps won't interfere with the humidification function.
You asked whether I have experienced a reduction of dough weight as a result of the proofing process. A long time ago, I did do some before and after weighings and there appeared to be some weight loss during proofing but my recollection is that it was slight. I also wasn't sure that my scale was accurate enough to really detect the difference.