Star Trek HAS only shown one version of the distant future. All other futures get wiped out and they never intersect, as far as I remember. For example, there's never 2 contradicting stories about the same distant future.
Think about it. Star Trek
is a franchise created by many different writers and producers. Nobody writing one story is going to know for sure what some future writer or producer may want to do in a later story -- or what they themselves might want to do a couple of years down the road. So there's a built-in pressure to avoid
imposing limits on the future, to leave things as open-ended as possible so there won't be anything restricting what future stories can do. So Trek episodes that give a glimpse into the future tend to make a point of leaving things ambiguous. "All Good Things..." ended with the crew specifically saying that now that they knew about that future, it wouldn't necessarily unfold the same way -- and of course it didn't.
So it's one of the core assumptions of Trek time travel that the future is absolutely not fixed, that there are many different directions it could take. Not only because it's necessary to avoid restricting future storytellers' choices, but because it's necessary to maintain a sense of danger and high stakes. All these stories about fighting to save the Federation or the galaxy don't carry as much weight if the future is already predestined. So since ST is a fictional franchise and the needs of drama and storytelling dictate its rules, one of those fundamental rules is that the future is always mutable. (Which is further reinforced by "Parallels," which showed that the timeline naturally, spontaneously diverges into many paths even without time travel being involved.)
And just because we haven't seen overt contradictions between our glimpses of the far future, that doesn't mean there aren't any. We really haven't seen enough of any distant future to jump to such sweeping conclusions. There may not be any proof that Braxton's Temporal Integrity Commission and Daniels's Temporal Agents aren't
in the same timeline, but there's no proof that they are
either. They're entirely separate agencies, one Starfleet and one civilian. They could be part of a common history -- I proposed how one could've led to the other in Watching the Clock
-- but there's hardly any proof that they are.