I agree. But it's not something that is going to change. SD want their sites interlinked, so as such so will the search.
I have said ever since the cross posting of the forums began (over 18months ago IIRC) that it is a bad idea, but it is how they wish to run things, i don't see it changing any time soon.
Oh..and when you said mixes all of stardock, i thought you meant just the search mixed em all up, wasn't sure if you knew the extent of the site sharing.