I can't speak for Gnome, but KDE makes it pretty easy to create rules that apply automatically to any new window that meets whatever arbitrary criteria you set.
That's terrible. That's an "unbreak my software" preference. User's shouldn't have to mess with that; things should just work in ways they expect, out of the box.
I disagree. With how KDE handles this, I'm not at the mercy of the software vendor's whims on what windows stay on top and which ones don't. I have complete control through a standardized interface that can even be automated if I wish.
Does it require a little more knowledge on the part of the user? Yes, but it's worth it because with that knowledge comes power.