I think it's because the females also have a penis?? too that they can like pull out or something, because if it's a female omega and female alpha together the omega can still get pregnant.
The world setting in omegaverse is very very diverse, and depends on the author.
In the explanation pages at the start of an OVerse you usually get the rules of that specific world. And female penis are never shown, but alpha women usually have one, it's never the topic, just background info, because it is yaoi afterall.
For example, in Kashikomarimashita Destiny conception is possible even in male betas and alphas. Also one of the characters there has two mothers
How did the male omega have a child if the alpha was female (I'm talking about the parents)? I've never seen that happen in a manga beofore