While the Sox do have spending limits, there are some $225mill spent on non-Pedroia players. And if free agency has taught you nothing else, you should have learned by now that merely spending on a free agent doesn’t always help the team. The list is long and affects nearly every team nearly every year.
If it helps, think of spending $14 mill on Pedroia as a preventive measure that will keep DD from wasting it on another player who not only won’t help the team, but also won’t be gone in two years.
The whole coach angle, if both sides wasn’t it, isn’t going to affect the luxury tax unless Pedroia willingly gives up about $25mill that the Sox agreed to pay him despite knowing the risks. And considering Pedroia did win an MVP award while making league minimum, I’d say he earned it. Let’s call it overdue backpay...