Missed this part?
"(UPDATE JAN. 17: With Mike Napoli reaching a one-year, $5 million deal with the Sox, the team now has even greater flexibility for future offseasons. However, with Napoli’s deal including incentives that could push the value of his contract back to the roughly $13 million annual average to which he originally agreed — albeit for one year instead of three — the Sox’ ability to stay under the luxury tax threshold in 2013 may hinge on his health.)"
So if Napoli remains healthy, they aren't $17M under.