Right--the authorization we saw was for the return trip, and the question was what that might have implied about the trip down.
The NTSB report notes that, earlier that year, during Tropical Storm Erika, the Captain felt no need to ask for authorization when changing course--he just made the change and notified HQ. This time, with his job on the line and future career in doubt, he seemed less willing to act independently.
The NTSB concluded that they had no solid evidence that the company was applying direct pressure for him to stick to the route, but they did note a whole host of implicit pressures, as well as a relative deprioritization of safety and crew management in the company culture as a whole, that might have adversely affected his decision-making.