Honestly, I don't remember TOS explaining the physics behind how the Guardian of Forever worked, or the Atavachron, or Janice Lester's mind-transfer device, or whatever the Kelvans used to turn the crew into paperweights. Star Trek
has never really been about rigorous hard science fiction, especially if it gets in the way of an exciting space opera adventure/morality play/drama/comedy/horror story . . . .
And, unless I missed something, the new movie still takes place in a future that basically works, where people from diverse backgrounds and worlds come together for the common good. Where people aspire to explore the cosmos as part of a United Federation of Planets. Sounds like STAR TREK to me . . . .
As for turning "utopian" into a straw man, you may use the word in a less literal sense (which I applaud), but I've seen endless debates on this very board about whether such and such episode or movie or book is "utopian" enough, or people stating confidently that there should be no disease or conflict or personal failings or political corruption or casual sex or child abuse or whatever in the perfect utopian world of STAR TREK, which bears little resemblance to the universe depicted in TOS.
So, yeah, I do think it's possible to get carried away with the "utopian" thing, at the expense of telling stories like "Conscience of the King" or "Is There in Truth No Beauty?" or "The Enemy Within" or "Court-Martial" or "The Ultimate Computer" that explore both the dark and light sides of the 23rd Century . . . ..