Presumably they took Miramanee's ancestors because they saw that the Native Americans were endangered by European diseases and colonization.
Which doesn't establish them as benevolent. Rather, this could be the classic case of "Air Raid"/"Millenium" where people who are doomed to die anyway are abducted at the last moment for nefarious purposes.
It would certainly be nefarious to place the native Americans on a planet where they will assuredly die if their asteroid deflector fails! But perfectly logical if the purpose was to breed them for slave labor in an (illegal?) asteroid mining operation, much as in "The 37s" and "North Star" but now with the extra twist of this deflector system that drops the incoming asteroids down to the planet in a controlled manner so that they can be mined without further need for complex tools...
TOS also suggested in "Return to Tomorrow" that Sargon's people were the ancestors of most humanoids, or at least Vulcanoids
...Or just the folks responsible for transplanting them to hostile worlds such as Vulcan, a hellhole seemingly incapable of ever evolving humanoids on its own?
Or, alternately, the folks responsible for rescuing the native Vulcans from extinction when their climate changed, by intervening and altering the Vulcan physiology to be desert-compatible - and therefore in practice the originators of the species?
Apollo's people were on Earth circa 2700 BCE, nearly five millennia ago. (Which is problematical in itself because that was 2000 years before the emergence of classical Greek civilization; the writers of "Who Mourns for Adonais" really dropped the ball on the research.)
One could rather argue that Apollo's folks left an impression that after two millennia resulted in the classical Greek civilization. It would be the Platonians who would witness said civilization in operation, much later...
Having Apollo and the other Gods be ancient even to Homer would be a good idea, allowing their images to be perverted somewhat, and their influence be less than literal. Note that Apollo himself only refers to Greek characters who themselves are mythical and ancient: Agamemnon, Hector, Odysseus. Assuming these folks are actual people, they could well date back five millennia "in reality" - possibly even in our reality, considering how vague the dating of the Trojan wars is, and how stories associated with those wars might in fact be legend carried over from even earlier conflicts.
Overall, it would seem that meddling with species that somewhat resemble your own, or remind you of your earlier form of existence, is a common pastime in the Trek galaxy - and involves a succession of meddlings across a timespan of billions of years, with the newly matured "adults" giving a boost to the newly emerged "kids" before fading away, letting the "kids" mature into "adult" meddlers. Whether such a process would diversify or unify the cultures and species is arguable...