After literally hundreds of tries and 3 solid days I have finally figured it out

I don't use Paris England's method (I asked him for his method and he kind of putted around the tree and gave me some response that is questionable

- glad he did because that was the motivation I needed) and I don't use Vanilla's method (I don't know what his method is either). The way I have figured out how to do it allows you to clone a waypoint and to SEE it in Goblin at it's respective room. This method does not use .prt files or modify them in anyway. The only edited files are the cloned ones. This method also specifies new waypoint_info, waypoint_edges, and animation_info for the cloned waypoints (so one can do what the please with the new waypoints without messing up original files). In the below screenshot you'll see Waypoints_Room_QR2 with a bunch of new waypoints added to it. You'll also notice that SR_WP04 (a cloned waypoint) has a sapiens attached to it. That sapiens is the guy holding the tank truck in the screenshot
And here he is in-game:
Now it should be easy to add new waypoints to dock and anywhere else