Well, I can see how there could be two schools of thought. Some fans believe that ENT is kind of like ST'09, in that it's a history created when time travellers from the Prime universe came back and interfered in events. Others, myself included, believe that ENT was always intended to represent the origins of the Prime timeline itself, to set up the events of TOS and the later series -- so that the "unaltered" future Daniels came back from was not, in fact, the Prime future of the Federation, but some slightly different version thereof. (Slightly different in that Archer managed to keep the temporal meddling from diverting the course of history too much.)
And the cool thing about Trek tie-ins is that they've never been required to limit themselves to a single uniform continuity, but have been free to tell different versions of the same historical event like Kirk's first mission as Enterprise
captain or the origin of the Borg or what-have-you. Different fans are always going to have different beliefs and expectations about certain major events, and any given version is bound to satisfy some fans and displease others. Which is the value of having more than one version available.
And that's why I haven't felt any need to coordinate my Rise of the Federation
novel -- which is part of the extant Pocket novel continuity -- with what Goodman has done in his book. I (along with my fellow novelists) am offering one conjectural version of the Federation's early history, and he's offering another, and the differences should be interesting and should offer fans a wider perspective than a single unified version.