I'd love to see how one comes to these number. $0.75 is either very expensive flour, or a very large loaf sold too cheaply. Adding seeds (at what, 5-10% of the weight of the flour?) to a loaf doubles the ingredient cost? Glancing at bulk commercial prices, sesame seeds added at (the unrealistically high) 20% of a loaf made with 500g flour should be about $0.29. Poppy seeds almost gets you there if you use the unusually high 2018 price, at $0.65.

$3 of bulk part-skim mozzarella is generously something like 250g worth. That's skimpy for a large pizza. The rest of the ingredients for this "good" pizza are free?

A bakery that's throwing out too much is baking too much, or there's no market for their bread. That's nothing to do with the margin on bread being thin. Small profitable bakeries are ubiquitous where there's a market for them. See: France.