I disagree, that wouldn't be a "smart" writing move within this context. If anything it would be more of a cop-out to make it omegaverse, an easy way out of exploring the themes and implications of what the cult is trying to achieve, the reasons for going about it the way they are, as well as the individual characters' experiences and development. There's already so much potential in the premise, in S. Korea of that timeline, a cult operating and gaining massive power while seemingly tolerating (encouraging even) homosexuality - among other unusual inclusivity -, is genuinely so intriguing to consider. Adding mpreg would deflate all the plot build-up, suspense and mystery by providing that as the singular, irrefutable explanation to all of it. The author is known for their nuanced approach, never providing an all-ecompassing answer. It would make little sense to suddenly sacrifice that just to include omegaverse in the story.
And I'll keep pointing this out: there are no physical signs of Seong Su having given birth, nor anatomical changes.
Author has been planting red herrings everywhere and I genuinely think they're having fun with people speculating and doubting whether Seong Su actually gave birth; something that could reflect the character's own doubt, actually, considering he's definitely been a chronic victim of manipulation and coercion within the cult.
I might be wrong in the end and I'll still enjoy the story to a degree even in that case. But the omegaverse thing would unnecessarily derail the plot and deny us of far more complex and twisted revelations and choices to come.
I'm on the fence, because like you said, there aren't any physical signs or changes that point to seong su having given birth in any plausible way, and this is a grounded, realistic story apart from this point of speculation.
that said, I do think that somehow having alpha/omega dynamics in the story would also serve the foreshadowing and themes being developed so far. there are too many references and allusions to gender and the birth rate stuff to ignore it completely. so much (if not the entirety) of the oppression of marginalized genders and sexualities aims to maintain a particular reproductive order by subjugating anyone who can possibly give birth and enforcing "heterosexual" behavior. if it were possible that previously "unproductive" pairings were suddenly viable, that would undermine the logic behind the rejection of non-hetero sexualities in the religious context, particularly in Christianity, because one of the mandate "to be fruitful and multiply".
standard omegaverse or the currently popular versions of it wouldn't be very feasible either, but a more grounded take on it as something artificially imposed on the world would allow a writer to makes more explicit commentary on the sex/sexuality expectations and oppressions that are baked into the concept of omegaverse.
it'll be interesting either way!

Guys I really doubt this is omegaverse, those symbols existed way before omegaverse was ever a thing and since this is a religious cult merging Christianity with another it is likely intended for that context. The Alpha and Omega are the first and last letters of the Greek alphabet, used by Christianity to represent God's eternal nature and sovereignty as "the beginning and the end." There is also a cross between them emphasising Christ's divinity.