Ben, a couple of things:
The USDA regulations apply for any school lunch program receiving funds or commodities from the USDA. This would be virtually every public school. It matters not if the child receives a free/reduced lunch or pays full price for the lunch.
In many, many school districts (possibly the majority, but I am not sure), the school lunch program has to be self-supporting, if not actually make money for the district. In the program run by Ms. MillCreek 1.0, the revenue from selling food has to cover the staff salaries, benefits, food costs, etc. Her program receives no money from the district, and in fact the program is used as a cash cow for the district. Her 'excess' revenues over costs are put into the district's general fund, which really ticks her off, as she could do great things on improving the program with the money.
Finally, a lot of school lunch programs are now outsourced and run by commercial companies, such as Sodexho and the like. They come into the district and promise the school board that they will make money for the schools, so a lot of districts have gone this route.
PS edited to add: a lot of the snack bars, coke machines or what have you are now operated by the PTA or student government as fund-raising mechanisms, and as such do not fall under the jurisdiction of the USDA and do not have to follow the USDA regs. They are not a part of the school nutrition program. When my kids were in high school, the school store and snack bar sold junk food. This also caused gnashing of Ms. MillCreek 1.0's teeth, since these siphoned customers with their money away from her lunch program.