A settlement IS an agreement between more than one party, but that doesn't necessarily mean NSAC and the fighter. NSAC can "settle" amoungst themselves. They can "settle" for USADA levied punishment. Etc.
Nick fought back and then they settled, the inital punishment handled out wasn't a settlement. NSAC appears to be attempting to avoid drawn out fights (like Nick's) by working with the accused party to reach a settlement (and thus avoid further legal issues).
Jones went to arbitration but no settlement was reached (
http://www.mmamania.com/2016/11/1/1...attorney-happy-nsac-doping-daniel-cormier-ufc) and days later the arbitration panel decided to give Jones "the maximum one-year period of ineligibility for his anti-doping policy violation." (
http://www.mmaweekly.com/jon-jones-suspended-following-usada-arbitration-hearing).
Basically, the NSAC got mud on their face from how they handled Nick's case, and since then are trying to avoid that. Conor's refusal to adhere to his punishment and refusal to fight in Vegas also doesn't make either him nor the NSAC look good. By reaching a "settlement" they can minimize these undesirable situations going forward.
Another benefit of calling a levying of punishment a "settlement" is it reads much more amicable, which ultimately is in the best interest of everyone.