I believe tha Blish worked from rough scripts when he wrote some of the episode adaptations, mostly those that appeared in the first 3 or 4 volumes. I think that's why some of those varied significantly from the aired versions that we are all familiar with - "The Doomsday Machine" being a prime example.
That's part of it, but it's not the full reason. The philosophy behind adaptations was different then too. They didn't have home video, and reruns weren't as common as they became in the '70s, so a lot of the time, the novelized version of a story was the only version anyone would ever see. Without any basis for comparison, there wasn't much pressure to make the adaptations faithful to the originals. Rather, the process of adaptation was seen more as creating a new prose work that was inspired by the film or TV work, but adjusted by the author to work better as a piece of prose, or to reflect the author's style and sensibilities. A classic illustration is Isaac Asimov's novelization of the film Fantastic Journey
, wherein he heavily rewrote the story and even changed the ending in order to fix the glaring scientific and logic flaws of the film. Philip MacDonald's novelization of Forbidden Planet
under the pseudonym W. J. Stuart is also substantially different from the film; it's told in large chunks of first-person narrative with only a single consistent viewpoint throughout each section, so many scenes that were in the film are told from a different perspective or absent altogether, and much material that wasn't in the film is included.
So in the early volumes, Blish was working under that standard -- not trying to be slavishly accurate, but using the scripts as the starting point for creating his own, Blish-style stories. So he felt free to modify their content as he saw fit and to tie them into his own work by throwing in references to things like the Vegan Tyranny, Bonner the Stochastic, and the Xixobrax jewelworm affair.
But Star Trek
reruns had unprecedented success in syndication, so they ended up being broadcast constantly and repeatedly, so fans were able to get to know them intimately. And that changed television by making reruns more commonplace (leading to a reduction in the amount of new material produced per season), and it also started to change novelizations, because fans wrote to Blish complaining about the liberties he took and wanting more faithful adaptations. Of course, the change was gradual; novelizations in the '70s and '80s were still quite free to take liberties, though they tended to hew closer to the original works. Vonda McIntyre's Trek movie novelizations added a wealth of new material and reinterpreted or corrected a lot of what was onscreen (such as correcting "Ceti Alpha" to the more accurate Alpha Ceti), and even Roddenberry's TMP novelization approached the material in its own distinctive way, and he's the guy who produced the actual film. Alan Dean Foster's novelization of The Black Hole
changed its ending. And so on. It's not like today where studios insist on absolutely slavish movie novelizations for some reason.