I don't mean this as offensively as it might come across, but where have you been for the last 4.5 years? Before Nike came along and the "best high school team in the nation" was decided by voters there were plenty of people who screamed for a team championship.
So Nike came along and created it. For the first few years FLN and NTN tried to thrive together (Footlocker even expanded to allow for top NTN finishers from the west who couldn't compete in the FL Regional) and eventually I believe Nike offered (not sure who initiated contact and what actual contact went down - it was more just hearsay) to merge with Footlocker and the deal never went through. Now we have Nike trying to take over.
Look, I don't get how there are people on here saying high school competition is about individual only. I would argue that in high school cross country should be more team oriented than at any other point in a person's career. That is the point where you have the most participation by those seeking friendship more than personal and individual accolades in the sport. The team aspect is born by this camaraderie and expressed to the fullest by those that have the individual drive for success that translates into team oriented goals.
As for the "how many run into this conflict?" The best teams tend to have the best individuals. One example is the three CA kids or so. One from the Dana team, that soph from the Loyola team, and the one that got second to him at the state meet. They were the 3 fastest at the CA state meet I believe and all accompanied their teams to NXNs. I don't think any of them really performed up to par by looking through the results, but there are still something like 5 or 6 CA kids going to Footlocker (none of the 3 fastest from the state meet). Just pointing it out...