genuine question, why do you tag "intersex yqy" if you're trying to say his genitals aren't relevant?
i had debated for quite a while whether to provide an answer to this, and have ultimately decided i will give you benefit of the doubt so as to take you at your word. if you wish to read more on this than some random tumblr post, i highly encourage you to.
"intersex" is a term for those carrying sexual characteristics (physical, anatomical, genetic) that do not fall in line with the boundary of sexual variation present in what is socially considered to be female or male. sex is a spectrum regardless of species, and designations for humans in particular are entirely arbitrarily constructed depending on the society. which does change and shift as time goes on. compared to its current self -- pre-colonial filipinos, and even present tribes, had/have vastly different views on the expression and fluidity of gender both for transgender and intersex individuals. while there were favored gendered work/activities for men and women, the boundaries were not as strictly enforced as they are today and there was acknowledgement of those who visibly differed nonetheless belonging. much of this is reflected even in their religious practices and beliefs: the fluidity of sex/gender/presentation (through effects of puberty, adulthood stress, and late life)
now, as many people think and what your own misconception seems to be is... that the visible changes are only to genitalia. this is simply untrue.
sexual characteristics that manifest come puberty also tend to reveal someone to be intersex. people who are comfortably girls realizing they now need to shave facial hair, or boys beginning to develop breasts -- these are fairly common occurrences. and it is completely natural. even those in older age, those experiencing menopause for example, will begin processing hormonal imbalance. the body's ever-changing! even "cis" individuals cannot uphold strict boundaries on their sex/hormones/ what have you.
when it comes to yue qingyuan, i believe he had this realization through puberty -- and i have it occur around the point where he finally splits from being a beggar to instead monitor the streets on behalf of the other slaves. yue qi takes advantage of hormonal changes with her voice deepening & breast hypoplasia to pass as a boy and better protect herself; it is only convenient that she eventually realizes he prefers being perceived as a boy and there on out posits himself as one with relative ease.
under my interpretation, the intersex situation is inseparable from yue qingyuan being transgender. gender is, as always, a social presentation. what can be immediately gleaned -- a deeper register, flatter chest, fat distribution, muscle growth, facial shape and lack of facial hair -- all contributes to how he's perceived and naturally include the pre-established intersex elements i mentioned above far before he is ever sexually exposed.
so, indeed, his genitals aren't relevant for most fics i write. in fact, i find that flattening someone, even a character, to their genitals to be a very poor and distasteful practice. i do not tag intersex yqy in the same manner someone might tag, perhaps, "lqg has a vagina" because that is not all there is. nor do my [character is transgender (or nonbinary)] tags exclusively indicate their genital situation as being pre/no-operation (or however pidw/svsss does it); rather, it is primarily to give a shorthand nod to their previous experience, as well as provide context for why others may mistakenly refer to them by the gender they are not.
as with many headcanons of mine, these are just venues for narrative/character exploration because i feel it enhances the experience and crafting elements like this to fit is something i really enjoy... that's all.