It wasn’t made for that, omegaverse’s whole concept is for flexibility if that’s the story the author is telling. Like in this case the story was about “fated mates” from a different universe so they used that as a trope to bring them together. I’m not saying it’s a good story but I am saying that there’s no point in questioning the dynamic other than this isn’t what you wanted to read. Essentially the omgegaverse places anyone regardless of gender on the same status as long as their secondary gender is the same case being that; yes there could be a story of an alpha conceiving a child etc etc but that’s not the story the author wished to tell they instead used it as a means for their couple to unite.
If this going to be an omegaverse at least make their role be opposite, omega should be the dominant one the in the foodchain and alpha is below of them all, and it would be unique if the alpha can conceive a child. Much better if both of them were alphas. Omegaverse was made to be in female gaze to like see men getting impregnated or being in reversed but this one is just complete bullshit.