I'm a dual Peruvian-American citizen having taken my American friends to Peru I can attest that, while controversial, that the cheaper fares are meant to encourage Peruvian citizens who may not otherwise be able to afford air travel on their modest incomes.
This is along the lines of Florida resident discounts at Disney World etc.
So to answer your question, the fine is per leg of the flightthe fine is per leg of the flight. You may be denied boarding of the flight all together. I know this is an old question but this can serve as future reference for anyone having this dilemma in the future.
Lastly, yes they check your residency status. If you hand them a US passport, they will automatically scrutinize you because the main proof of residence is the DNI (Documeno Nacional de Identificacion). If you don't have that, or the foreign residence card, you will be assumed to not be a citizen of Peru. Of course, your ticketing agent may ignore it but you're essentially handing the information at check-in to get caught. Should you do an online check-in, then it is probably possible.