The reason is that in top-level windows in a plugin avoid taking focus unless the actual top-level component has this flag set (regardless of whether the subcomponents inside it want focus). This is to avoid taking keystrokes away from the host unless you really want them.
It’s not a perfect solution, but I can’t really think of a better one at the moment…
I’ve just been looking at this again, and have checked in something that might help. I’ve made it a bit smarter so that hopefully only the main plugin window will avoid getting focus, and not other ones…