A clone is not the same as an alias. To clarify what Shane said, the clone does not reference the original asset, although it references the same dependencies. In other words, if you were to download a locomotive off of the DLS (which downloads all of the requisite dependencies), installing the CDP of your cloned asset (which would NOT be a clone then) and right clicking "download" on it, would download the required dependencies as well. If you cloned the dependencies and referenced your new dependencies, of course you would need the new dependencies.
If it REALLY bothers you that they show as clones in CMP, take your CDP and reinstall and overwrite your existing version and it will no longer show as a clone. I frequently clone my assets when I make new versions, whether I just make a new skin or if I add an entirely different mesh- you download it, and it shows as "not a clone", but it is still a clone on my system. Probably 85% of my stuff I created shows as being a clone because it comes from the same starting point.