I did not see the point in grouping them at the top in the first place.
The main difference with grouping them, as I see it, is that expanding one replaces any other that was previously expanded. I never used the auto-expand feature in previous versions, so I don't know if this was possible before; however, now it's impossible to have them all expanded at once.
Personally, I think I'll find this a good feature, as I don't get any use out of having them all expanded, and usually find myself manually closing tree items I'm not using. However, I don't see the logic in not having documents, (or anything else which doesn't support drag 'n' drop between groups), grouped.
As KingSparta said, it's most likely a space thing. Perhaps smaller, more condensed icons with integrated text could be designed with less space around them, which would allow Documents to be included in the grouping system. Maybe even Services & Plugins too...?