
In this interpretation of the society, Alpha are considered top class citizens while Omegas are seen as inconvenient because they go into heat and thus lower class

What Anon said^ There are alphas families that would rather keep their blood "pure" so they want Alpha x Alpha instead.

I think Masaki's case is pretty rare, since usually the alpha genes should be dominant. I see it happen a lot in omegaverse stories even when it's a Beta x Beta couple. There are times where the kid end up presenting a completely different gender than their parents even if one gender is really dominant from the both of them.
Why did the father not want his alpha son to mate with an omega? Is that not the ideal partnering?