I see this is an old request. Anyway, here is my situation. Currently I am working on both:
diagrams that will stay in yEd or go to Word and required white background.
diagrams that will go to Powerpoint, on a dark background template.
I am usually working with both cases in the same session, making it unfriendly to switch back and forth changing the global preferences.
In the end I export to GIF (neither PDF nor EMF yield transparent backgrounds, pity) and transparency works OK. But while editing I have to jump through hoops with my white labels on white background.