ABO is mainly used as an attempt to separate gender and sex more explicitly than our real society does. Female Alphas being women who are sexually male, and male Omegas being men who are sexually female.
So they're trans. But in a weird, biologically essentialist way that means that you don't have to admit it or understand real world trans experience. Cool.
So much of the ABO setup, here, drips in the possibility of trans allegory, but the actual implementation makes it hard to map to meatspace. There are three genders... But then let's immediately separate the genders along sex lines, so that gender is different from but still intimately related to sex. Both men and women can get pregnant... But dominance and leadership are deliberately tied to the ability to impregnate people, and the ability to get pregnant is treated, in and of itself, as a moral good. This is extremely frustrating, because I can see how these ideas play into wider narratives about how men and women are supposed to behave, reinforcing negative stereotypes. Like, I suppose it's good that omegas (the stand in for the "woman" role) are horny, but that's really all I'm getting out of this.
(Also, to be clear, what I'm hearing about general ABO tropes are much more problematic. Like, tying the presence of a penis to leadership is... Gross. So so gross. But I'm trying to keep my discussion more focused on this particular manga.)
The story doesn't seem to rely too heavily on the ABO stuff, though. At least, so far. We spend a lot of time on ABO exposition, but there isn't a lot that's really related to it otherwise. MC finds out that there's a hot girl at school, goes looking, finds her, falls in love, is rejected, pursues it gently anyway. Not an uncommon yuri story. Most of my worries are about what "defective alpha" and "Physical characteristics: beta" end up meaning. Based on a lot of the discussion of ABO tropes here, I worry that it's going to mean she doesn't have a penis, which... Clearly isn't a real problem, even in the fictional world, since they still know what yuri is.