Yes I suspect the keyboard shortcuts will bother me too. One of the things I like about Elementary is that there are a bunch of things bound to Command out of the box. They also refer to it as ⌘, which has a nice familiarity about it.
The underlying Ubuntu still refers to it as the Super key, but elementary uses the clover to symbolise it when it can. Still can't get to Mac like setups, though - apparently in Linux it's the applications that intercept the Super key, so it's never going to be possible to get a consistent experience.
Window managers definitely get a first crack at keyboard input. For example, I have a bunch of super-related keyboard combos set in i3wm that always go to it. I doubt that's the problem you're referring to. More likely it's that the window manager has no consistent means to make any given window/app do anything in particular, like copy or paste. The app decides its own key combos for those. There's no universal way to do it globally short of using nothing but apps that are specifically intended to work with gnome or kde or another uberenvironment's configuration system. Basically, you could bind super-c at the WM level, but you couldn't make it always copy.
