Yes, we know the book presents itself that way. The suggestion is that maybe, in the TrekLit universe, Jake Sisko wrote this as a work of fiction and presented it as an epistolary work in which he interviewed the participants in an alternate history -- just as Bram Stoker wrote Dracula as a collection of journals, interviews, and articles even though it was actually fictional.
I suppose it's possible. Then again we do have multiple timelines going on in the Trek universe now. Who's to say that its not entirely true to its particular universe?
Personally I don't think there should be an attempt to reconcile the two timelines. We have the Prime Universe, we have the Abrams Universe, there were millions of Enterprise-Ds in Parallels. Leave them be.