Boeing is a business and this is not the first time a regulated business has clashed with a regulatory agency regarding regulations, directives or policy.
This might be the case for the fuel tank issue. The FAA issued a directive. Boeing disagreed. They fought the good fight but in the end, the FAA did not back down.
The other issue, the one of incorrect fasteners, is more troubling. Here, Boeing actually identified the problem and put together an action plan to implement a remedy. But they failed to do so. It's one thing to take a stand and argue for a position. But in my time there, all too often, they just figured that they could put off the inevitable remedial action. Or worse yet, implement it, wait for the regulators to sign off on an inspection and then go back to the old way of doing business.
The basis of self certification is that when a company says they will do something, they follow through even if they aren't hapy about doing so.