Since I'm not on my work computer, I can't cite any of the documents. But a lot of it has to do with button and box alignment, especially when there is an unknowable number of elements, each of unknown length. As mentioned in my previous comment, grid isn't possible because I have to support a sizable number of IE11 and WinXP visitors.
One example of where things fall down in Flexbox is when you have a number of boxes/buttons in what is, to the user, a grid. If you use justify-content: space-around to match the designer's specifications, you end up with orphans centered in the last row.
To meet ease of reading guidelines, those orphans should be left-aligned. I think it looks like low-grade dog food, but there's a lot of eye-tracking research that shows people ignore items centered in the last row because they think it's decoration, or an ad. If it's left-aligned, that signals that it's part of the rest of the grid.
It's in these cases that inline-box is still the best way to go.
Speaking of ads, one thing I've learned in the last two years from all these research studies is that pretty much anything put in a right column is ignored. People have become inured to ads there that they nearly always assume that content is an ad, even if it's navigation. So one of the big guidelines is that navigation is always either 1, front-and-center; 2, top-line; or 3, left column, even in right-to-left languages.