Probably not Linux specific.
That is expected for now; running Big Picture in a desktop environment is in addition to the desktop client functionality, not instead of.
This happens even running fullscreen..., it's annoying.
Hello @oblitum, you're probably looking for the more recent issue being tracked at #5286.
@kisak-valve thanks for pointing that.
Nothing extracted yet.
In windowed mode, big picture opens a chat window from the normal client. (and we still have those ugly notification boxes instead of the beautiful ones from big picutre).