I am going to give you an A+ on this one.
I couldn't find any notes on the "stuffed" feature but I did find some private messages that I had with Mike (Boy Hits Car), with whom I worked in creating all of the dough calculating tools, including the deep-dish dough calculating tool. I also remember what we were thinking of when we added the stuffed feature. The stuffed feature was actually an afterthought that came to us toward the end of the design of the tool but the idea was simple: to come up with numbers for a single dough ball that could be divided into two smaller dough balls, with one of them (the inner dough ball) being used to form the skin in the pan and the other (the outer dough ball) being used to form the top skin that is draped over the pan and trimmed and pinched to the skin in the pan. At the time, we struggled on what part of the larger dough ball should be allocated to the top skin. There weren't that many members who made and posted on stuffed pizzas at the time and there was little hard data on how much dough was needed to form a top skin. But, based on what data we were able to find, and to add the stuffed feature while we had a chance, we decided that 25-33% of the total dough weight was perhaps a reasonable range. However, I think what happened is that the percent number put into the box calling for that number was taken with respect to the outer dough ball rather than the total dough weight. However, I think if one stays within the 25-33% range, they may still be OK. What I subsequently learned after watching a video at the Travel Channel on how Giordano's makes their stuffed pizzas is that the top skin appears to be considerably thinner than the skin placed in the pan--thinner than I originally thought--almost to the point where one may not even know that the top skin exists. So, it may be that the smaller dough ball weight (outer dough ball) in the deep-dish dough calculating tool is a reasonable value to use. I was hoping that members would come back with feedback on the stuffed feature, but that did not happen.
I don't know whether it will be possible at this point to change the tool. Everything that is done on this forum is by unpaid volunteers. And once such a valued volunteer leaves the forum or visits only infrequently, we lose the contributions of that volunteer, including doing fix-ups. Mike and I worked for months on the various tools, and there were several hundred data points that Mike had to program in order to bring the tools to fruition. I am aware of only one other error, which, fortunately, was not one that would hurt anyone's pizza.
Even though the stuffed feature is not used as much as the rest of the deep-dish dough calculating tool, I appreciate your bringing the matter to the forum's attention.