My understanding (from one of the many books on TOS I’ve read) is that it was not originally adapted from Brown’s story. Gene Coon wrote it (and I’m not sure if it was ever established that he had read the story) with peace being made. Sometime during production they discovered the Brown story, and because of the similarity renamed the episode to match and gave Brown credit. I vaguely remember Brown being very pleased about this. Certainly the episode ending is more in keeping with the world of the series than Brown’s.
The books, by the way, are not quite novelizations - there are two per book, and they are written by Alan Dean Foster. They give a lot more detail than Blish’s short story versions of TOS episodes, but are not as well written. I think there were six put out, I have at least five of them. I seem to remember a bunch of the original pbs collected into a larger hardcover book some time ago.
At the time they came out, I seem to remember reading that Larry Niven was on the writing staff, which explains the appearance of the Kzinti and the Soft Weapon adaptation. I’ve never confirmed this, though - is he on the credits of the laser disk version?
(One of the best things about getting cable 18 years ago was that Nickelodeon ran TAS back then!)
I forgot about Arex… I haven’t read the New Frontier books in a year or more and I don’t think I’ve even read the Gateway crossover. I was thoroughly confused by M’Ress being on the Excalibur when I picked up the book (Restoration?) following it.
Same thing happened to me with the relaunch of the DS9 series. After so many years of the books being independent novels, they decided to make multiple issue story arcs and it was disorienting at first.