I find it hard to see any good reason to believe any of these stories – they seem very designed to point blame in any direction other than one where there are deep pockets. The NYT article seems especially dodgy to me since blaming airmanship is an unhelpful analysis and suggests to me (always) a rug corner being lifted up to sweep something under.
Even if airmanship was a contributing factor, the appropriate analysis should be looking at what could be done to avoid further cases of stunningly poor airmanship.
The Kegworth crash, over 30 years ago, is very instructive here as the pilots survived and lost their jobs, due to being blamed for poor airmanship (they turned off the good engine, not the faulty one). But when it turned out that they had had no training in some key differences between the 737-300 and the 737-400, it became clear that the crash was a failure of design, not of poor pilots. (For those not familiar with the story, they had almost no data in the cockpit to identify the faulty engine and turning off the good engine also turned off other systems that made the fault in the other engine go away - so it seemed like they had done the right thing - but when they needed extra thrust to land the faulty engine failed completely. This is the crash where passengers knew which engine was faulty but said nothing when the pilots announced which engine they had shut down.)