Per Jules Ernst’s post, Firefox 41 follows Flexbox’s
order declaration, but NVDA 2015.2 did not (even when paired with Firefox). I think Firefox is ultimately going to follow the other browsers and honor source order. I cannot speak to JAWS, VoiceOver, etc. I am happy to have people leave notes of what they find.
Regardless, your point about making sense visually is accurate. Expectations can be set by visual layout, creating an even bigger problem for a sighted keyboard user. That becomes even more apparent with Grid using the example I pulled right from the spec.