How do we know the Relativity crew DIDN'T do anything?
I mean, we know they had to come clean up the mess left behind by Harry's actions at the end of "Timeless" (they called it the 'Temporal inversion in the Takara sector) so perhaps they did the same thing here too. Just because we didn't see it in the episode doesn't mean they didn't do anything.
For all we know, ten minutes after the end of the episode (onscreen), the Relativity cleaned out every last bit of extra tech and left the Voyager crew wondering where it went. In fact they probably DID do exactly that.
What else does the episode Relativity prove but that if they don't like how things turn out, they go back to a saved point and do-over their mission until they save the day.
Exodus, every timeline, whether it be the Federation or not, has some species/race/alliance which masters timetravel first and leaves the universe to patrol outside time and regulate the progression of continuity... Trouble is, that I'm assuming that there is only "one" the same outside of time that every temporal power tries to dominate. that even divergent Earth histories are not going to recognize the totally alien authority of their almost selves that the shit is really going to hit the fan if the Tholians of the Klingons gain the high ground.
So even if the timecops from Captain Janeways Timeline were superhappy about Endgame, the Time cops from Admiral Janeways Timeline would have been shitting their biscuits, and those timecops would have had to have had a smack down to see whose universe had a greater right to exist.
Unless 29th century Earth is temporally shielded and it cannot be altered by schisms and paradoxes within the timeline, which they would be fools not to.