It seems like the Occam's Razor on Nola is more that he was hurt last year, and that superseded any other issues he'd been having (like pitching from the stretch or adjusting to the clock and now ABS). It often takes a full season to hit your stride (despite Zach Wheeler showing otherwise) and Nola's obviously trying to figure out what does and doesn't work about his stuff at his current age.
And it seems like the minor league staff did a great job with Painter this year. The same applies to him really, last year was his "learn to pitch again" year, this year - however slowly - he's put it into practice.
Not sure Alvarado has any issues that he hasn't always had. Between the PEDs, his constant struggle to stay in shape, the suspension and the injury last August he was never a great bet to come roaring back, but not picking up his option and signing another reliever wouldn't have been a great bet either (as Keller has already shown).
They may not look like dopes for standing pat at the deadline but hindsight still says they were pretty big dopes for not having more SP depth at the beginning of the year (even if it was reasonable to think Walker could be replacement level). andy frequently suggested Painter should not start the year in MLB, but there was never anyone else with Wheeler out.