Game development takes a long time, and they needed their story set in place before the novels had been even conceived of or commissioned. They were actually pretty consistent with the Lit at the time that gave development began, but I think there's something about Ro (?) that contradicts even the DS9 relaunch. They did use some Lit characters and ideas, though.
Either way, to keep things consistent, the alternative would be for the game devs to decide the next few decades of TrekLit, and make that be consistent with the game, but given the story they did come up with, I'm personally glad TrekLit is free to chart its own direction.