I suppose they make it that way because sometimes it may get confusing for a child to have two dads, and having to call them 'dad' at the same time. I guess there are other words to call your dad, but simply 'dad' or 'daddy' are commonly used on younger ages.
It may also be due to the fact that usually a woman is the one giving birth, so perhaps theres an element that to a baby, calling the one who gave birth to them, their 'dad' may not have the same effect.
I don't prefer a child calling their birth parent mom even if they're male, in a gay relationship, honestly I'm equal on both sides. If my gay friends decided to adopt a young child, I wouldn't really care if the child called one of them mom or not, it's up to the child really.
I think it has more to do with the fact that pregnancy is involved so there's still somehow a distinction between the parents and the word "mom" is not necessarly only related to women anymore. it would have that far less meaning irl. That being said I too prefer when in omegaverse both are called daddy, it's less confusing

I like how the kid calls both of them daddy and not mommy unlike other omegaverse. This is how it should be