More importantly, it breaks what we now know of real astronomy and physics. "Megas-tu" was rooted in the continuous-creation theory of cosmology that was a rival to the Big Bang theory. When it was discovered that the universe was expanding, some physicists couldn't accept the idea that the universe was of a finite age and had a specific moment of creation, so they postulated that maybe new matter was constantly being created out of white holes in the centers of galaxies to replace the matter that moved away as the universe expanded, so that the universe was in a steady state. This was already a largely discredited idea when "Megas-tu" used it, except for a few theorists who clung to it, but it was finally disproven conclusively by satellite observations of the cosmic background radiation. So now the idea is as outmoded as canals on Mars or dinosaur-filled jungles on Venus.
To compound the problem, multiple later Trek productions have referenced the Big Bang (Voyager was even taken there by a Q once), so we know that theory is true in the Trek universe, which means "Megas-tu" couldn't have happened as shown.
I don't care for stories that posit that the victims of the Salem witch trials had actual magic powers or the equvialent, because it's ascribing legitimacy to a lie told in the name of persecuting and victimizing women. But at least "Megas-tu" uses it as an allegory for persecution and prejudice, which makes it somewhat excusable.
Alan Dean Foster's novelization described her simply as "the most beautiful girl in this or any other universe." He was just trying to conjure up a fantasy woman to make out with (at the very least).
I read Memory Alpha's description of the writing process based on writer Larry Brody's account. Apparently it was normal for Roddenberry to rewrite every script, just as it had been on TOS; that's a head writer's job, after all. Although I'm surprised, because my understanding had been that Roddenberry pretty much blew off responsibility for TAS and left it to D.C. Fontana to be the effective showrunner.