I have learned a lot from this thread so I'd like to post my story and hope it can help others. Background: I had a non-PUP X up for delivery.
Before taking delivery, I asked my OA to order the part for me (gave him the part number), and initially he said the service center has one in stock. However when I ask him to place the order, he told me once he dug deeper it seems that Tesla has changed process and this parts can no longer be installed on non-PUP model X.
Knowing that I can't get what I want, I told him it's fine. Then at the delivery day (8/30/2018), I directly spoke to service and parts, asking to buy that part. Immediately they said they have one in stock and they can sell it to me and even asked if I want it to be installed for additional $40-50 (the cashier wasn't sure about the labor cost). I said sure if you can install it right now. A very nice tech is nearby and heard our conversation. He said he can install it right now. He even explained that they will not be able to enable the software button but the filter will fit with no problem.
So 15 mins later, vola, I have the HEPA filter installed! They even waived labor fee since I just took delivery!
So the moral of the story is, don't give up easily. Try reaching out to service and parts in person, and maybe you will get surprised result.