Maybe, but the Atavachron didn't change them - they jumped through before Atoz had the chance to process their bodies for the change. It did nothing to their bodies, they simply landed 5000 years in the past.
That's not exactly they way they say it happens in the story. The way the atavachron/time portal evidently works, the reversion is automatic and fatal unless the traveler is prepared. It's not fully explained, but preparation either makes the reversion safe, or not as severe, or both. In this story, both matter and life patterns from the present are at least slightly unstable when transfered to the past. Phasers don't work and cells revert to their nature of the era. It's a relatively novel take on the idea of time travel. Only a prepared traveler is viable in the past.
There are many possible interpretations of the author's intent, if any, but one I've thought of is that she might intend certain physical laws to change subtly over time. Preparation by the atavachron either compensates for this, or prevents the transition from being fatal, but apparently it cannot be undone. Otherwise, what is now can't exist then, and what is then can't exist now, so to speak.
You don't have to agree, I'm just stating what I've thought of about the episode. There is a level of fantasy in effect here. But, to me, the deliberately daring and original aspects of the fantasy about the nature of time travel were refreshing, especially when compared with many other episodes produced in the third season, and a lot in the second too. In my opinion, this episode is superior to certain episodes from every season.
for the sake of giving Spock a gf.
Spock needed a qf. And Zarabeth was totally hot.