I'm guessing Boeing, even if it's just by virtue of having been around so much longer than SpaceX, has greased a lot more pockets than SpaceX. Consequently, while NASA has no horse in the race, I'm guessing plenty of well connected people in and around NASA have a horse in the race.

the horse they have in the race are their 2 stranded astronauts

and to be honest, if spacex had made the shuttle that was assigned to boeing they would probably have made it work. no plan survives contact with the enemy and no engineering design survives its own prototype. the people working at these companies and managing the teams is what made the difference, not nasa's original design