Perhaps the "only way they know how" is the limiting factor for some time travel stories to have "overwritten" timelines? The technology and knowledge available to the time travelers limit their visibility to only specific timelines which to them would appear to be an overwritten timeline that needed to be "fixed". Their actions, even though it "already happened" in the alternate timeline unlocks their way back to what they would consider their timeline.
We've seen in TOS that their time travel ability and visibility could appear to them that they needed to fix the timeline to get back to what they believe is their own in "City on the Edge of Forever". The Guardian is controlling their travel and the surrounding space. Even the slingshot maneuver may also be limited to only going to specific timelines which would give them the appearance that they can change or overwrite history. Whereas warping through a quantum fissure in "Parallels" gives a more unrestricted timeline jumping process but isn't available until TNG and not without fixing the sickness that comes with hopping quantum realities. How this plays out in Enterprise's Temporal Wars and who determines which timeline is the reality of consequence, I don't know...