It seems STO can't even keep it's tie-ins straight.
I don't see it as any different from the situation with early tie-in novels like Ghost Ship
for TNG. Tie-ins written before the debut of the things they're tying into have a tendency to be best guesses, and one shouldn't really expect them to be authoritative sources.
There's also the fact that TNotM was written by a freelance novelist for Pocket, someone whose knowledge of the STO universe was secondhand (and necessarily limited since the game was still in development when he wrote the book), whereas the stories in the magazine are by the actual head writer for STO itself.