Magic as an essential tool for pre-industrial genetic engineering has been widely used in two franchises: Geneforge and Ravnica. Additionally, your description of women is reminiscent of the Bene-Gesserit.
The Geneforge series by Spiderweb Software follows a conflict between the Shapers and their creations. The Shapers are a sect of magicians who learned how to use magic to create and manipulate life. First they learned that magic applied to certain reagents (such as a reptile egg) would modify the embryos within. Through massive amounts of trial and error they learned which applications of magic produced optimized results such as breathing fire (Fyora), semi-intelligent servants, or entire ecosystems. Then they learned how to magically charge organic reagents into a universal reagent: essence.
Eventually, they learned how to create a (magical?) microscope. In doing so they were able to view the fundamental 'scrolls' (DNA) in all living things. Then by mapping these scrolls and tracking what changed with magical application, they learned how to vastly improve their techniques in a targeted manner rather than through endless trial and error. This culminated in the creation of the Geneforge, a pool of essence designed to rewrite and augment the scrolls of a shaper or creation.
In the Magic The Gathering plane of Ravnica, a city covers the entire plane and is controlled by 10 guilds. One of the guilds, the Simic Combine, was created to preserve the health of all life-forms on the plane. Eventually, one of its Guild Masters, Momir Vig, decided to lead the guild in a new direction: to improve life. Drawing upon their study of life, medicines, and biomancy. In particular their biomancers uses biomancy to mutate lifeforms or create new biotools such as the Cytoplasts.
In Frank Herbert's Dune Saga, the most active and prominent faction is the Bene Gesserit. They are a powerful and ancient order of women with a host of physical and mental abilities that earn them the moniker of "witches". In particular, by taking a poison that brings them to the edge of death, they gain the ability to control their internal biochemistry and access the memories of their female ancestors. The former enables them to create an antidote to the poison before it kills them. Those who fail this 'trial' die. In several instances it's pointed out that their biochemical control enables them to create poisons, or alter pregnancies up to and including determining the gender of their child.
You state the following:
Women are able to use magic by absorbing energy from a parallel dimension called the aether.
Magic is slow and complex, taking minutes to hours to perform.
In this scenario, pregnancy would be treated like a long spell, taking the course of months.
Taking after Geneforge, these women can use trial and error to modify the zygote, embryo, or fetus. and track which applications of magic creates preferable alterations.
The mother can literally feel the life growing inside of her, and can communicate with it in some limited way.
It follows that the mother can track which applications of magic created which effects. (Cause > effect)
Keeping track of this information and teaching it to new initiates much like the Shapers of Geneforge would enable them to build upon the knowledge and refine their processes. Furthermore, as Henry Taylor suggested, it would be optimal for these women to refine and optimize their child's life organ (and/or create the organ in a male child).
Furthermore, I recommend you refine your definition of her internal sense of the pregnancy and communication. The level of sensory input will strongly determine their ability to make precise changes and record/confirm the result. Similarly, the communication opens another door. Do you mean she can communicate with the unborn child? At what point (embryo, brain development, etc...). Similarly why is she able to sense the pregnancy as opposed to her own body, and at what point can this enable the same control (or at least sense) of biochemical control like the Bene Gesserit?