The difference is this: TNG was written and set after TOS, and failed to mention Tellarites, which is one kind of writer's mistake. ENT was a prequel, and included too much that would never be seen in TOS, since it was already done. But Nu-trek assumes ENT in it's background, so it's easy to just say "Timeline 1: TOS and TNG+", and "Timeline 2: ENT & nu-Trek", and just assume Riker has access to a holodeck program based on scans of the Guardian of Forever.
But I really don't have a problem with the idea that TOS is timeline 1, TNG+ is timeline 2, and ENT/nu-Trek is timeline 3. I just wish they'd get a good writer for plot and stop going for kewl factor.