"One" in the name represents only a numerical designation for the building, as there are other WTC buildings as well. I don't get the creepiness you feel.
I don’t really think it’s creepy, but it is likely that the numerical designations of the surviving WTC buildings will not be changed. Therefore, there will be a 1 WTC, and a 3 WTC, but no 2 WTC. Not necessarily creepy, but it is a reminder of what happened there on 9-11.
BTW,
You seem to know more about the WTC than I do. There was another building besides 1 WTC and 2 WTC (the twin towers) which did not survive the attacks on 9/11. Which one was that?