This has definitely changed. I'm using the current mainline kernel and it includes proper configs for the BBB. Works pretty much hassle-free.
Problem was to support capes (addon boards) especially dynamically and at runtime wasn't really supported in mainline. They had special cape manager patches to do it but it wasn't a good solution for upstream.
3 years later or so we finally have good overlay support for this in a mainline happy and now merged way. They paid to have this work done which is great, though sadly took a long time.
I forget the guys name that did it but he is clearly a champion of patience.