The only non-window-related weight considered in the formulas above is the weight of the skin itself. (In the paper, the formula for skin weight is the formula for the surface area of a cylinder times skin thickness times density.) So the paper is really saying that the weight of a skin without windows is 25% less than that of a skin with windows. It doesn't take into account frames, bulkheads, or anything else that makes up a fuselage.
There are probably some structural savings that the paper doesn't take into account. But the total savings can't be anything like 25% of the weight of the fuselage as a whole. I don't think TD's going to be called to make good on his guarantee.