Lost in Space
It's your world, your rules, you can do whatever you want. It's magic; no scientific consistency is required.
"It's Occam's Shuriken! If the answer is elusive, never rule out ninjas!"
Perhaps, as the title suggests, carrying girls to terms takes far longer than a boy? Like, maybe boys take the normal nine months to gestate and be born, but girls take eighteen months at the least, with said pregnancy being more difficult than normal (more cramps, longer morning sickness, all those unpleasantries basically worsened). Definitely makes the mother consider her options lol I guess it would make sense for the mother's magic to become weaker when pregnant with a girl, since that magic is likely putting great effort in the gestation. Combined with the double length pregnancy, it sure makes a downside for being pregnant with a girl
Other, hilarious options: It is not any harder to birth girls than boys, and since more magic means the economic payoff of being a mother to girls is way higher - Your kids are also your apprentices, and the work they do until they leave home makes you richer and safer so you have a world in which the gender ratio is massively, ridiculously lopsided.
Most boys being born at all only because someone is going to hand over a massive dowry in 16 years.
The typical household is 4 to 7 women sharing a husband, depending on how heavy the local ratio is, and the primary romantic literature of the nation is not so much about the men, it falls into two categories - Novels about women striking it so very rich they can afford to pay a dowry and support a husband that is not ever going to be able to enchant more than seven self-propelling cart-wheels per day, and novels about the hunt for sister-wives you do not mind sharing with.
(female) Bisexuality is considered a blessing from the deity, lesbians are quietly envied, and being a gay man is economic doom. You better be an amazing artist or something, or you are screwed.
I can see all of that happening except for a skewed gender ratio, unless there's also sex specific abortion practiced regularly in this world. That whole gender ratio doesn't logically follow from anything else you suggested.
Now, saying the magic makes males rare among mages for some reason does, but there's also non magic people in this world supposedly, which could add another wrinkle of complexity to the whole scenario.
(Also A Brother's Price cuts through the whole sister wives things by literal sisters marrying the same guy so.)
The "Mother chooses gender" bit was taken from the thread starter - I just thought it would be more fun to not try and balance things, because imbalances are obvious plot drivers.
Googled Brothers price - sounds fun, on the pile of interlibrary loan requests it goes.
In this world, human beings have access to magic, which is a slow and ritualized process. However, girls are born with more magical capability than boys. As a result, females mages are far more powerful than male mages. four male mages would be equal to one female mage in terms of power. Pregnancy is viewed as more of a long spell, and the sex of the child can be biologically determined by the mother. i want there to be a downside to this. What biological consequences would there be for carrying a girl to term?