There is a big difference here: Previously, NASA basically received what they requested in the contract specifications. The Atlas V was what the USAF specified

There is a big difference here: Previously, NASA basically received what they requested in the contract specifications. The Atlas V was what the USAF specified in the EELV contract. The SpaceX Falcon 9/Dragon was designed by SpaceX, driven by Elon Musk's requirements. The part where the design matched what NASA wanted for the COTS program was a happy coincidence, but NASA were not driving the original design specifications. Of course, the F9/Dragon was adapted to NASA standards, and is also an effective satellite launch vehicle.