Of course most GSA city pairs are subject to a contract. The whole point of the city pairs is that all government employees flying that route will use the specified contract carrier. If there is low compliance by employees, the carriers will be less likely to submit favorable bids for "exclusive" rights that in reality are not.

The fact that you never got caught doesn't mean that the command would have approved it if it knew. There has been increasing emphasis on compliance over the past decade.