Just giving you the reverse argument. For example a research contract is not the same a s a contract for goods. Will Beoing ever pay back the development costs to the Feds? Royalties to the taxpayer?
Do pharmaceutical companies pay back their R&D to consumers? Do automakers?
Why do you single out Boeing because their customer is the government?
As to paying upfront, this is common in many business practices -- custom clothing, contractors, legal retainers...