Yes, the offer is only good for new customers buying together JFK + KORD + Zurich. In that case, Zurich will be free.
I think that's just normal in any business...I still recall having bought my original Xbox1 on launch date, and it was 479 EUR...
Speaking about Flight Sim specifically, there's a new package just coming out called "FSX Gold", which includes FSX + Acceleration Pack, at the same price that FSX only. Of course, existing FSX or Acceleration customers wil not get any discount, but new users might be tempted to pick it up. As I've said, it's pretty normal. Zurich is a 10 months old product, so we though it might be worth trying a sale on it. Note, the sale will end on October 15th, after that, Zurich will go back to the original price.