CarMax is not the cheapest option, it never was. Their whole business model is to sell the car at a good-enough price, and to make the sale frictionless. And they've succeeded.
Today they are the market leader, but as the article suggests, if they start to use that leverage to sweeten their markup too much, other competitiors will come along and offer something better.
This is really just a news article about how a free market works.