It's not genetic. It's hormonal. Pony fetuses have "magic tissue stem cells" in them, and the mother's conditions determine how they express. Her genetics, but also other factors. The mother's diet, the weather, and other factors also change her baby's developmental process.

Some hypotheses.

Pegasus birth conditions:

Pegasi eat foods that can be easily foraged or transported.

High altitude, low oxygen, lots of sun and wind, and it's really cold up there. They're probably very exposed all the time too.

Emotionally, I bet they hate being impaired by the issues of late stage pregnancy. They have a very strong value on athletics.

They can probably stay mobile, stimulated, and physically fit, with the help of clouds and wings.

They are constantly surrounded by cloud magic and flight magic. Their environments are completely saturated.

Now for unicorns.

They can build some pretty serious shit, and I bet they can make great prepared food with that telekinesis of theirs. Maybe it's even magic food.

They are less impaired than pegasi in some ways, and more impaired than others. They can't move as well, but they have no problem doing whatever they feel like that doesn't involve physical activity.

I have a feeling that their big castles and cities aren't as regulated, weather wise. First off, mountains have a major effect on weather. Pegasi can emulate the effects of mountains, but here they would have to constantly work AGAINST the effect of a mountain. A unicorn city in an unfortunate geographical location might be very dreary and rainy.

I don't really know what to say about unicorn culture re: pregnancy. The whole idea of them being the ones who care about class and appearances might be relevant but I dunno.

There is a lot of magic all around them, but mostly their own. Or perhaps their friends like to shower them with magical gifts?

And finally, Earthers.

They canonically have the ability to make prepared food, and that makes some amount of sense given that living on the ground gives then the space and resources to build windmills and threshers and whatever. They also have a ready supply of cultivated food.

They live at low altitude with a highly regulated climate thanks to pegasus weather teams.

Pregnancy has gotta suck for earth ponies. They have next to no ability to stay mobile.

As such, there's probably a strong cultural value on caring for mares who are having rough pregnancies and becoming sedentary. Being pregnant would be a positive experience, minus how much it physically sucks, of course.

They have little or no magic in the places where they live and work, or depending on your model of earth pony magic they might have earth pony magic in the places where they work, and they won't be working as often as usual.

As such, foals are likely to be born as either the mother's race or the race befitting the cultural and physical surroundings. This even explains the racial makeup of individual locations.

What do you fellas think?