I'm using it from the beta1, and I must say that it is awesome; apart from those notifications zero-interaction zero-configuration, I hate them!!!
I'm running 10.10 and it's the same as you describe. Which I think is the right way to do it, for anything that pops up unexpectedly.
Thunderbird (and others) doe notifications the way you describe, but I don't think ubuntu (or any other distribution, or even osx for that matter) ever let you click directly on the system-wide notifications.
Ubuntu swapped out the common notification daemon for one called notify-osd.