With respect to Paramount "sign[ing] off on their status" in the White Wolf City book (September 1996 edition), that's not quite as clear-cut as Ellison implies. The copyright notice reads as follows, italics as per the indicia:
The City on the Edge of Forever (original Author's version, not rewritten shooting script as aired), by Harlan Ellison. Copyright (c) 1975 by Harlan Ellison; extended version copyright (c) 1995 by The Kilimanjaro Corporation. New material included in this edition copyright (c) 1995 by The Kilimanjaro Corporation. All rights reserved.
After copyright notices for the "Perils of the City" essay, it says:
Star Trek is a Registered Trademark of Paramount Pictures.
This implies that Ellison acknowledges that the
shooting script is not his property, just the "original" and "extended" versions. What this means as far as ownership of the characters and storyline means, I don't know.
edit: Though, I guess David Mack does!
Sorry, took forever to research and type all this up, so by the time this was posted the point was already made and more succinctly.
With respect to the 2004 MBA (and who knows how this may have looked back in 1966), there does exist a clause (16.B.3) that says:
Writer shall retain all other rights (hereinafter referred to
as the “reserved rights”) not expressly referred to in
subparagraph 2. of this Article 16.B., including, but not
limited to, dramatic, theatrical motion picture,
publication, merchandising rights, radio rights, live
television rights, interactive rights as provided in Article
1.C.19.c.(2) and television sequel rights (other than the sequel rights mentioned in subparagraph 2. of this Article
16.B.), and Company shall only have the limited interest
in such rights as hereinafter described.
Adaptation of the work in the form of books don't appear to be specifically listed anywhere and could arguably fall under the definition of either "merchandising rights" or "publication rights" (both of which are defined in article 1 of the MBA).
Elsewhere there are clauses that allow the studio ("Company") to buy out the author's rights in these areas.
However, clause 16.B also states:
Company agrees that separation of rights as provided in
subparagraphs 2. and 3. inclusive of this Article 16.B.
shall be accorded to the writer of a format, story, or story
and teleplay for any television motion picture (other than
one of an established serial or episodic series) provided
that the terms of this Agreement relating to rights in
material apply to such format, story or story and teleplay
as provided in Article 2 hereof. If, at the time of the
transfer of rights to the material so purchased, there is in
existence a valid agreement for the publication or
dramatic production of such material, then, for the
purpose of this Article 16.B., such material shall be
deemed to have been published or exploited. It is agreed
as to an established serial or episodic series the Company
shall own all of the rights in the material of any nature or
description whatever including, but not limited to, the
right to use the same in any field or medium whatever
without obligation to the writer except as provided in
subparagraph 14. of Article 15.B. with respect to
additional payments to be made for specific uses.
Basically, it says for an
episodic TV show (as opposed to a TV movie)
the studio owns everything.
The critical question to me is whether or not this same clause existed back in 1966. If yes, then Ellison's argument is much weaker (unless for instance Trek isn't considered an "established" series).
Clause 15.B.14 referred to at the end of that section does outline certain payments due if, for instance, a movie or radio show is adapted from the story, but that doesn't mean ownership of the material is retained by the writer, just that s/he should be compensated fairly for any adaptations. For instance, 15.B.14.m states:
If the Company licenses or grants to any third party the
merchandising rights to such material (as described in
Article 1), Company will pay to writer an amount equal
to five percent (5%) of Company’s net receipts (as net
receipts are defined in subparagraph g. of this
subparagraph 14.) derived from such merchandising
rights. Comic books, magazine publications, comic
strips, cut-outs, and other activity books shall be deemed
to be included as merchandising rights.