No, the heads of federal agencies are external because they're political appointees. High profile jobs go to donors and those who have supported the politician in charge of the appointment.
*Some federal appointees. The head of FAA under Trump was Stephen Dickson, who was an F-15 fighter pilot in the U.S. Air Force, then a pilot for 27 years at Delta Airlines before becoming Vice President of flight operations [1].
The current head under Biden is Billy Nolen, a former pilot who flew the Boeing 757 and 767 and worked as an airline executive for years before joining the FAA [2].
By credentials, these two are definitely qualified.
I think the original point being made was that having such extensive airline industry experience actually makes you unqualified to lead the FAA. For instance, Dickson, through his position at Delta, has likely developed strong ties to counterparts at Boeing. This made him unable to adequately address the safety issues of the 737 MAX.
My follow-up point was that experience in regulating airlines is more important than experience running an airline when it comes to leading the FAA. However, those who regulate airlines as a career are unlikely to be big political donors, so they're unlikely to be chosen to lead the FAA.