Airsupport .. I don't know your background but it appears not to be related to any certification areas.
MFS (who is an aircraft designer chappie) has put the story pretty succintly in my view .. the general idea is that the OEM designs an aircraft to do a job and uses Industry standard techniques (with the occasional push to new technology) to design his bird. Along the way the internal system checks that the design standards (FAR25 and the like) can be satisfied.
Sometimes the OEM will endeavour to design more from the standards than from general practice and that can produce interesting results including both good and bad but, at the end of the day, it is a mix of those who know how to design, designing, with a view to getting the requisite tick in the box from the certification world so that the bird can be sold in the marketplace.
The reality is that the world is competitive .. therefore Brand A doesn't unilaterally make Brand A's product incredibly stronger than Brand B's .. as MFS has indicated .. the result is a steel girder bridge with no commercial value.
The pilot is required to be trained and licensed ... the operating techniques adopted by operator and pilot should be in accordance with the techniques recommended/required by the OEM/Type Certification.
Simply wishing that a transport category aircraft can be treated like an aerobatic machine remains just that .. wishful thinking .. the two animals are very different and the required operating techniques, likewise, are quite different.
It is not a case of the OEM having to second guess everything an enterprising operator or pilot might do ... rather, the OEM states what should be done ... the operator or pilot who wants to do something different without OEM blessing is out on his own.
.. and, then again, every now and again, technological status is challenged for the imperfect animal it is ... as, for instance, with Comet, etc.
Each of us in the game has his/her role to play .. it is a team effort ... except in those rare cases of gross incompetence or wilfully negligent behaviour it is not a case of assigning blame within the confines of the Industry (although the legal system may well do independently and in parallel).