You have illustrated that teams use it to to gain more favorable terms for the team. As I've stated before, a NTC clause would not be as valuable to players if it only blocked when a team wanted to trade.
Because the bargain is not, "You will not be traded, here is a NTC", the bargain is, "you will have control over where you will play." In that case, the player is indeed holding his end of the bargain, he took less money and longer/shorter term than he wanted for the benefit of the team, in exchange for the ability to control where he plays.
Because the team agreed to give him that right for something they wanted in the contract.