I like these paths to 2409, but drives me crazy at the same time.
They use some stuff from ST novels, but not others. I know the novels are not cannon.
In the Titan Novels Suran was killed by Dontra, while all the events of Baregs death agree with what was written in the supplement to 2387.
They've stated already that while they are using the novels as source material, it's just inspiration, at best. The novels aren't canon, so they lack the weight of canon media, and besides, Cryptic's trying to make their own game, with it's own storyline, rather than just copy what everyone else has already written. I'm just glad they're acknowledging good series like the Titan one at all rather than just dismissing it, like most Star Trek media does (apart from novels, obviously). So while you will see deviation from the books, it's relatively minor, like Suran's death. They even did it with the Countdown novels; by not mentioning specific details, like Worf getting stabbed, they can leave it up in the air whether or not they want that outcome (i.e., if canon Trek kills Worf off, but since Cryptic has been developing his character in STO timelines, they can still keep him in by not following the Countdown by exact detail). So there are benefits to it, as well.