Not exactly. Guideline #9 doesn't apply only to the finished film:
Creators of fan productions must not seek to register their works, nor any elements of the works, under copyright or trademark law. [emphasis mine]
Pretty sure a screenplay qualifies as an element of the work.
But the implicit question here, I think, is does guideline #9 apply at all with respect to the registered material under discussion, if there is no Star Trek fan film with which Jenkins is involved that uses that registered material (assuming for some reason that CBS chose to take action against Jenkins)?
I think it's reasonably clear that Jenkins at one point intended to be working on the fan film with Peters and that he created and/or contributed (from work(s) he had previously written) the portions of the screenplay under discussion for that purpose. If I understand the sequence of events correctly, there was a falling out with Peters, and then evidently to deny Peters use of the material under discussion that Jenkins had contributed, Jenkins registered that material he had contributed minus Star Trek IP with the Copyright Office.
Still, the implicit question here is, does guideline #9 apply to Jenkins with respect to this registered material, if he never uses it in a Star Trek fan film? You said a couple of posts ago that CBS has no interest in pursuing Jenkins over this screenplay, and that it is devoid of Star Trek IP. How could guideline #9 be applicable here under all of these conditions?