If the Federation time-cops are so set on preserving the timeline, why did they allow the timeline to be altered to such a degree that the Eugenics War, a major event in Humanity’s history, happened at least 30 years after it was supposed to.
For what it's worth, I wouldn't characterize them as "allowing" the timeline to be altered. They seem to be hard at work fighting to keep it as intact as possible.
As far as being a "separate timeline", it depends on where you draw the line. Being strict about it, one could argue that every single instance of time travel creates a separate timeline, so we witness dozens of assorted timelines throughout the shows, starting all the way back in the first season of TOS. Generally, however, we tend to refer to timelines as distinct only if there are substantial differences in the course of history, and "substantial" is subjective. In-universe, there definitely seems to be a certain degree of "good enough" when it comes to "restoring the timeline", even if minor changes persist. Until we see a substantial contradiction of events between SNW/PIC and TOS/TNG/etc, I'd say it's premature to declare them completely separate timelines.
(And, from a production perspective, it certainly seems like the intent is that SNW and PIC are "prime timeline". SNW just had a time travel crossover with LDS with no apparent references to crossing into an alternate timeline, and PIC S3 was filled with direct references to the events of TNG.)
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