While I absolutely 100% agree with you, isn’t this dude an ultra dominant alpha? There’s no way his pheromones won’t affect ANYONE let alone a beta aka someone without a definitive second gender. If you imagine Alpha as blood type a+ and omega as blood type b+, beta is a blood type o-. Dominant genes DO push other genes to the side to make space for themselves so in this case, it makes sense that it happened.
That being said, it absolutely is subtly homophobic and we see that a lot with yaoi by making everything a beefy top x vaguely feminine twink bottom. I’ve read stories with Alpha x Alpha and Alpha x beta and even beta x Alpha recently. Don’t give up on the subgenre. It totally does exist and it’s amazing!

Chapter 9: Ok so he’s becoming an omega.
I fucking HATE when authors do this. It’s such a cop out. And in a strange way kind of homophobic.
In the omegaverse, if alpha omega relationships are socially acceptable then those are the “heterosexual” relationships. The true homosexual relationships then would be things like alpha beta relationships because, in this story especially, those are frowned upon and deemed socially unacceptable.
And we hardly if ever get to see that because the authors always fucking make their betas into omegas.