Looking over the birth events, there are a few events other than the eating one that can affect the baby's traits
If you are Christian, Muslim, Norse, or Tengri, there is a once-per-dynasty chance of getting a vision about the baby. A good vision prevents all negative congenital traits and sickly. Additionally, Christian and Muslim good vision babies get either attractive or quick, Norse good vision babies get strong, and Tengri good vision babies get shrewd. On the other hand, Christian bad vision babies get left-handed and extra intrigue, Muslim bad vision babies get hunchback and extra learning, Norse bad vision babies get blind, giant, and extra intrigue, and Tengri bad vision babies get feeble and extra stewardship.
There's an event where the bay can kick, and if the mother hopes they are a warrior, they can get +2 martial and have any negative congenital traits removed.
There's an event for pagans where you can throw a fertility festival, and the most expensive option is quite likely to remove all negative congenital traits and gain attractive.
If the mother is a drunkard or a hashish addict, there is a chance for the baby to be slow, have slow upgraded to imbecile, have quick removed, or have genius downgraded to quick. If that happens, the mother may get an event to kick the habit.
A pagan mother can get an event to offer a sacrifice for the child, which gives a chance for them to become strong, attractive, or quick, depending on your choice.
A Christian mother can take a vow of chastity, humility, charity, or temperance. If you keep that vow (don't have a trait opposed to it), it can remove sickly and all negative congenital traits. This is more likely if you have a trait that matches your vow. Afterwards, you may get an event about keeping your vow, which can give you a trait related to the vow. If you refuse, there's a small chance the child may become sickly.
With the weird cravings event, if looks like there is a base 10% chance of getting it. It's more likely if you have less than 3 children and none of your children have harelip, ugly, or clubfooted or if this is her first child. It's also more likely if the mother is hedonistic or gluttonous. It's less likely if the mother is temperate, or has 3, 4, or 5+ children already. It's also less likely if pregnancy flavor events are set to limited in the rules.
If you select one of the foods, there's a 70% chance for them to gain the congenital trait, but also get +2 to a stat (Clubfoot and diplomacy for quail, harelip and intrigue for hare, and ugly and learning for trout)
If you are the mother and aren't gluttonous or you are the spouse and aren't greedy, you can pay extra to have her eat whatever she wants, which doesn't give any of the penalties, but can give gluttonous. If you are the spouse and are greedy, you can just refuse, which will upset the mother and may give her stressed, but won't risk congenital traits.
Of course, all of these can be prevent by turning pregnancy flavor events off, which may make pregnancy work the way it does without Holy Fury.
If you are Christian, Muslim, Norse, or Tengri, there is a once-per-dynasty chance of getting a vision about the baby. A good vision prevents all negative congenital traits and sickly. Additionally, Christian and Muslim good vision babies get either attractive or quick, Norse good vision babies get strong, and Tengri good vision babies get shrewd. On the other hand, Christian bad vision babies get left-handed and extra intrigue, Muslim bad vision babies get hunchback and extra learning, Norse bad vision babies get blind, giant, and extra intrigue, and Tengri bad vision babies get feeble and extra stewardship.
There's an event where the bay can kick, and if the mother hopes they are a warrior, they can get +2 martial and have any negative congenital traits removed.
There's an event for pagans where you can throw a fertility festival, and the most expensive option is quite likely to remove all negative congenital traits and gain attractive.
If the mother is a drunkard or a hashish addict, there is a chance for the baby to be slow, have slow upgraded to imbecile, have quick removed, or have genius downgraded to quick. If that happens, the mother may get an event to kick the habit.
A pagan mother can get an event to offer a sacrifice for the child, which gives a chance for them to become strong, attractive, or quick, depending on your choice.
A Christian mother can take a vow of chastity, humility, charity, or temperance. If you keep that vow (don't have a trait opposed to it), it can remove sickly and all negative congenital traits. This is more likely if you have a trait that matches your vow. Afterwards, you may get an event about keeping your vow, which can give you a trait related to the vow. If you refuse, there's a small chance the child may become sickly.
With the weird cravings event, if looks like there is a base 10% chance of getting it. It's more likely if you have less than 3 children and none of your children have harelip, ugly, or clubfooted or if this is her first child. It's also more likely if the mother is hedonistic or gluttonous. It's less likely if the mother is temperate, or has 3, 4, or 5+ children already. It's also less likely if pregnancy flavor events are set to limited in the rules.
If you select one of the foods, there's a 70% chance for them to gain the congenital trait, but also get +2 to a stat (Clubfoot and diplomacy for quail, harelip and intrigue for hare, and ugly and learning for trout)
If you are the mother and aren't gluttonous or you are the spouse and aren't greedy, you can pay extra to have her eat whatever she wants, which doesn't give any of the penalties, but can give gluttonous. If you are the spouse and are greedy, you can just refuse, which will upset the mother and may give her stressed, but won't risk congenital traits.
Of course, all of these can be prevent by turning pregnancy flavor events off, which may make pregnancy work the way it does without Holy Fury.