The self-certification process (airworthiness certificates) is the manufacturer (rather than the regulator's inspectors) stating "this one specific aircraft with serial number _______ has been built according to the design covered by its type certificate". Nothing more.
In other words, an airworthiness certificate only specifies that a specific aircraft is airworthy /because/ it is built according to an airworthy design. Whether the design is safe or not has always only been up to the regulator to decide. In this case, the regulator dropped the ball and approved an unsafe design. If Boeing was not allowed to self-certify their own aircraft, the FAA would still have issued airworthiness certificates for them, including the two aircraft that would have gone on to kill hundreds of people, because they were built according to the design the FAA approved.