I need to fix this, or Blizzard needs to fix it :P

On my end, I should use cooldown:SetSwipeColor(r, g, b, a). That will take care of the most obvious bit of the cooldown, but it doesn't handle the shine effect when a cooldown ends.

I've fixed it, via reparenting the cooldown if a bar happens to have zero opacity. I've not adjusted the actual opacity of the cooldown, because I think that could stomp on things like OmniCC.