I think it represents the varying levels of perceived risk in delivery, and a tacit acknowledgement that SpaceX is simply operating (at least) 2x as efficiently. If SpaceX fully delivers on their contract, I hope we see Boeing squeezed harder next time. What would be even more interesting is if SpaceX were to hit the finish line on time and budget, and Boeing getting lost in billions of cost overruns and delays. The article talks about "cost+" accounting, so that may play a part in how this happened as well.
In the end I like that they awarded two contracts. There really is nothing like good competition to motivate everyone.