I would argue that the "breakthrough" (such as it was) was the fact that women were there at all and that some of them were department heads or held positions of considerable responsibility. The show was supposed to be in "the future", but the writers were in the present.
True enough -- but as I mentioned above, there were other TV shows on the air at the same time that did successfully show stronger, more assertive and independent female characters. Rand doesn't just come off badly compared to modern female protagonists, but to a number of her own contemporaries. As I said, the myth is that TOS was on the vanguard for its era, but while it was making an effort to be inclusive and progressive, there were a number of other contemporary shows that did it significantly better. And sometimes TOS cancelled out its own progressiveness with some really blatant sexism.