You have to read a little ways into the article to get more complete information:
It noted that 42 FAA employees oversee 1,500 Boeing employees with certification authority. Internal Boeing documents previously released showed Boeing employees, including a key official in the certification effort, mocking the agency and slamming the aircraft's design.
The document notes that Boeing and the FAA were looking into "concerns about undue pressure on" Boeing employees who had FAA authority to sign off on aspects of the plane. It said that future reports on the delegation process would be forthcoming.
42 FAA employees, and 1500 (a fraction of the total Boeing workforce) Boeing employees. More central to the facts of the matter, and the article, is that the 1500 "Boeing employees who had FAA authority to sign off", are, as subtly mentioned, delegated by the FAA. So, though they receive a paycheque from Boeing, they are (within the scope of their FAA delegation) responsible to the FAA, not Boeing - they wear two hats on the job. Each person is individually evaluated by the FAA under 14CFR 183.29, and is accountable to the FAA for the findings of design compliance that they make as a delegate of the FAA. Though these delegates of the FAA are employed by Boeing (or any of a number of other similar organizations), they are not "Boeing". In theory, Boeing has to approach the applicable delegate for their signoff on a design change, just as they would approach the FAA.
So, why does the FAA delegate to a company employee? Because the FAA realizes that while carrying out its role to support and promote an aviation industry, it cannot possibly afford to pay the salaries of all of the people required to evaluate and find compliance with an aircraft design. 1500 government salaries, as opposed to 42 - just for Boeing? That would be a lot of tax dollars? And, the concept of delegation goes much farther than just findings of design compliance for certification, how common is it that a flight test, or other pilot ride is with an FAA employee? Know knows of an FAA employee issuing a C of A for an aircraft, or doing an import/export inspection? The FAA delegates lots - just this is in the spotlight, and for good reason.
What Boeing and the Boeing employed FAA delegates did during the certification effort of the MCAS obviously missed the mark. The FAA employees were apparently unaware. But this:
The report also faults the Federal Aviation Administration for poor communication and notes it handed over the vast majority -- 87% -- of certification responsibility to Boeing.
Misrepresents what actually happened. The 87% certification responsibility was not handed over to Boeing, zero responsibility was handed over to Boeing. the 87% responsibility was handled by FAA delegates (1500, it seems), who are accountable to the FAA for their work, and are paid by Boeing. I expect that some account will be taken of this, as there will be records and signoffs....