Competition yellows, love 'em or hate 'em, do not (not intentionally anyway) help or hurt a particular driver in a pre-planned, contrived way. Yes, it helps the show, but helping a particular driver/team is not its purpose. Each team has, theoretically, an equal chance to gain or lose positions due to a comp yellow.
Honestly, I thought the rule change was necessary. What Bowyer did was inexcusable. What the Captain did, on the other hand, was "The Unfair Advantage." Of course, the Captain has done other things over the years that have shown us why he is the Captain. The stories about the 4 vs 5 lug wheels and the elevated gas cans from Mark Donohue's days are epic.
NASCAR put Gordon in the Chase to right a perceived wrong. He got jacked through gamesmanship that was really unfair. That was more of judgment call. If I had to bet, I think NASCAR felt that someone messed with their product, they felt offended, and felt that they had to take action. I think that the Penske situation would have been a non-issue had we not had the Bowyer fiasco to kick things off. And they may have let Gordon stay out of the Chase, but the way it came together, I think they made the right call.