Hypothetically if we compare the biological development of a fetus, they all start with female traits that later develop into male traits (this is why men have nipples). SO in omegaverse, the omega-trait could be in all humans, but develop differently at birth or throughout puberty. An alternative possibility could be that he could be considered intersex, where his sex trait is hidden and can appear if triggered or very specifically looked for.
Maybe he's a beta but his numbers is just a little bit lower or higher for him to be considered as an omega. (ex. O=3.14 to 6.15, B=0.1 to 3.13 and his original # is 3.13) And here's the factor of the pheromone shower of an alpha and a dominant at that. Normal alpha can also turn any beta to an omega with an extended exposure. But since the alpha here is a dominant and the omega's number is already at that point it wouldn't be a surprise if the alpha pulled him to be an omega. And about your question about the reproductive system, everybody has it since beta can also reproduce and maybe it remained stagnant if not developed/used. The same way he was being exposed to the alpha pheromones, his internal was also developing at that point. And you asked what makes him omega aside from the scent, it's the heat cycle and the need to be mated with an alpha.
That's my understanding. And sorry if it's a mess. Lol.
I'm curious how does omega transformation even work? Isnt the prime characteristic of an male omega the fact they have wombs and can give birth?
Does he have one, if so where did the womb come from then, did it pop out of thin air?
Or does he not have one at all?
What makes him an omega now other than the scent? Someone pls explain