From the linked article…
So here’s what this essentially is: fans who love TNG filling in the gaps of the original story they love with the unexplored rest of the universe of people who would have been impacted by that storyline. That’s important for two reasons. First and foremost, this doesn’t take anything away from Paramount’s Star Trek production, and in fact does the opposite. The project doesn’t replace the original episodes, but rather builds upon them. In other words, this project could only possibly serve to draw more interest to Paramount’s product, since the book isn’t going to make much sense to anyone who hasn’t seen the original episodes.
Link crossposted from https://entertainment.slashdot.org/story/23/08/31/057243/paramount-dmcas-star-trek-fan-project
Wasn't the issue with this one that money was changing hands in exchange for a printed, physical book? Like, I know the team wasn't making money, but it's understood in fanfic circles that this is a Bad Idea and this was a very high profile (and, sadly, professional-looking) project.
The work is now on AO3 alongside countless other Star Trek fanfics that exist with no trouble. If they'd done that all along, I suspect there would never have been an issue.