I've only watched the Netflix series to date, but supposing Napoleon's comment is right:
I can only comment on what I know from the books, but there the mages actually draw energy from their surroundings, specifically the elements. And the prevalent attitude seems to be that there's generally enough of it around.
– Napoleon Wilson
I would hazard that the answer is in the "controlling and shaping chaos" part. If magic is a bike, then the flower is the training wheels. It is there to absorb the improperly controlled chaos and its consequences. As such the rock levitation lesson is about learning to sense and control the chaos without getting hurt, just as training wheels help you learn to balance and steer a bike without so much risk of falling over. Once they can do that properly, the training wheels can be removed, and the bike ridden and manipulated directly and safely.
For another analogy, the side effects are like pollution from the magic factory. By default, that pollution is poured out where it's made, directly into the mage. But with training you can learn to reduce it and pipe it away. Do it right and you won't see anything bad happen at all.
This possibly ties in quite nicely into Filavandrel's accusations that humans have polluted Chaos and synthetically generated it. The synthetic generation is presumably a reference to Aretuza's eels, and possibly other similar locations and methods. But the pollution claim may be almost spot on with the above analogy: rather than try to achieve some balance via naturalistic magics, they simply learned to dilute the negative effects and shunt them away. Geralt says Chaos hasn't changed any and the humans just adapted better: the eels and "pollution" may seem unnatural to Elves but it's not changing anything about how the world works, it's just making use of how that world works in a clever way.
The main shortcoming of this theory: why does the enchanter/surgeon still caution Yennefer that all magic comes with a cost before enchanting her? He's a mage, highly skilled in his particular craft, why doesn't he just shunt this "cost-pollution" away? The best I can say to this is to refer to something Geralt says during the dragon hunt
The people who made us, they made us sterile for a lot of reasons. One of the kinder ones is because this life isn’t suited to a child.
So the sterility isn't there for a single purpose. It serves many purposes. Possibly this particular magic of enchanting is so intense or complicated that there's no simple way of getting around a sacrifice. But why it must be a sacrifice of her uterus isn't limited to, or even derived, just from the enchanting's strict requirements. Methods of control and constrained loyalties are implied by Geralt to be the less kind reasons: loyalty to family would get in the way of loyalty to the order, caring for children would get in the way of performing your duties, etc. As such sacrificing the womb may not be strictly necessary, but it is sufficient. Yennefer also says during the Djinn storyline that she did not understand what that would really mean to her later. So she may have simply accepted the requested cost of her womb and fertility because she knew there had to be some cost, and at the time that seemed acceptable. Power, recognition, beauty, going to Aedirn instead of Nilfgaard as she desired, etc. Those are the things she valued then and got in exchange. It wasn't until later that she grew disillusioned with being a court mage and attributed value to motherhood, and suddenly what she sacrificed seemed greater than what she gained.