OP asked a practical question for a friend. I don't think that he needs a debate about the vagaries of the way the world ought to be.

Bottom line answer is that if he has a choice and has not yet booked, he ought to have the air carrier (or travel agent) book the tickets exactly as the passport is issued. But, middle names, initials and the like are not an issue and certainly not for TSA.

Thus, John Q. Smith and John Smith are both fine. However, Passport issued as Fred Q. Smith and ticket issued as Fred N. Smith might be.

Silly arguments about TSA are also not the only issue here. As an international passenger (I presume that as OP is located in Denver, that his friend is located in the US), the friend will be required to show his passport to the air carrier at least at check-in and likely at the gate as well. He will also deal with immigration formalities in Costa Rica and CBP for the return. None ought to present a "middle name problem".