My biggest issue with the whole thing, however, boiled down to the set of incentives that centered around individual performance. You see, the teams weren't _teams_ per se, but a collection of individuals working on their own projects, sometimes related to those of other teammates, sometimes not. A team-oriented process like Scrum or Kanban cannot survive in an environment where every person is optimizing every decision for their advancement/bonus/whatever. There's some exaggeration here, but I definitely saw a lot of this at FB. Having come from a company with high-functioning Scrum and Kanban teams that worked together to achieve a common goal, I'd choose that any day, JIRA or not.
This is obviously a single example and many of the issues were Facebook-specific. But I bet there are other, not so positive, sides to the "no process" story at the rest of the companies.
Note I'm not claiming that the Agile processes are by definition good. I've seen plenty of bad implementations as well. At the end of the day, every group of humans is different and may require a different process (or no process at all) to maximize their success. What I'm suspicious of is the "every team picks their own process" claim, having seen company-set norms exerting enough force to make deviations from the common pattern rather painful and counter-cultural.