The revenue tix will absolutely be subject to a change fee and fare difference add/collect. The reward ticket will also likely be subject to a change fee.

While you think that you are saving the company money by not flying a segment that really isn't the way that airline pricing models work. jetBlue may sell a cheaper fare from IAD-AUA than JFK-AUA to compete with another carrier in that specific market. Or price the non-stop higher because of the convenience of such a flight over a DL routing with a connection in ATL, for example.

Taxis and car services are about the only mode of transit I know where the fares are truly directly tied to the distance traveled. Airlines are about as far from it as you can get.