So the timeline is radically different, but somehow the Enterprise is exactly the same. How does that work?
exactly the same. Where are Worf and Troi? Tasha Yar is alive. The point is that if even one vessel has incurred significant changes, it's likely that the rest of the universe has, as well. It's a scientific fact that the amount of entropy in the universe is increasing, not the reverse. Applying this rule to an alternate reality, the degree of deviation from the status quo (the primary universe) would have increased over a period of twenty years, not decreased or remained largely unchanged.