The reference to "self regulating" is grossly misleading - one could even say deceiving - of the actual Boeing/FAA relationship. In fact the Al-J program was loaded with statements that, while not technically false, were intentionally misleading. Typical tabloid "journalism"
I've been a DER (now an AR - but it'd basically same thing) for over 25 years. I doubt any of you have gone through or realize what's involved in a new aircraft certification program (I've been through two and am currently involved in a third) - and although Boeing is now a 'delegated' organization, the level of FAA and EASA scrutiny is higher than ever. While "findings of compliance" can be delegated, Safety and Safety related items are nearly always retained by the FAA and EASA. There are countless Issue Papers, Special Conditions, etc. that all must be closed with the FAA/EASA prior to cert.
BTW, the push to make the manufactures "delegated organizations" came from high up in the government, and is intended to relieve the FAA of certifying 'routine' changes and free them up to focus more on the safety aspects and new technology, both during the certification process and in-service.