Correct. What you viewed was the renegade/director cut version. It omits all mention of them as aliens.
For a laugh, do a YouTube search for the fairy tale ending they made for this movie
Here's what I always wondered. In the scene when Katana takes over the subway and everyone is flying backwards and such, there's a split-second shot of a guy's head that looks like a puppet head. I thought I heard that his head explodes due to the force or whatever, which is so cheesy that I want to see it. But it's not in the old VHS release "The Quickening" version, nor in the Renegade or Special Edition. Does that actually happen in some version? If his head doesn't explode then why did they use a puppet at all?