Yea is really little so he copies his dads and how they call each other. Plus if u look back to Ch. 39 when Yua is an egg Seme calls Uke a mom and he says to not call him that. So they probably won’t be calling each other that.
I hope this answers this a bit. But it never fully states anything.
Do they explain why yua doesn't call them fathers? Or is that just not a thing in this world?