What seems reasonable to me is M/F/N where N is not capable of reproduction due to some kind of outlying error, so they cannot be a part of sexed reproduction. Are they omitted?
Sex and reproduction seem binary to me and most people. We should ignore technological or medical assistance and sort those results through the gender buckets which are more important to how they are perceived semantically, as you said.
In biological terms, sex may be determined by a number of factors present at birth, including:
the number and type of sex chromosomes; the type of gonads—ovaries or testicles; the sex hormones; the internal reproductive anatomy (such as the uterus in females); and the external genitalia.
People whose characteristics are not either all typically male or all typically female at birth are intersex.
My concern is that people are attempting to use the existence of intersex folks (at widely varying claimed incidence rates) to make faulty arguments about what is and is not normal physiology.
The criticisms are more about terminology than the core argument though - they mostly argue that "intersex" should only cover a small number of conditions that result in an arbitrarily substantial differentiation from a "normal" male or female, rather than any significant differentiation. So if the question is about sexual dimorphism, those criticisms are mostly irrelevant.
But here's a question: why is it important that they can reproduce? Gay men and women are unlikely to reproduce either, so should we ignore them in policy-making too? Are gay people abnormal?
There are several cultures that have arisen independently and have had more than two genders. Many of them are still extant today, despite the best effort of colonialists.
So that's gender down.
Intersex individuals exist. Intersex conditions range from physiological to karyotypes with variant sex chromosomes.
Transgender individuals are very varied but there are indications that it is partially heritable with genetics and the prenatal environment hypothesized to explain some of that.
And that's biology.
I could write a 100 page essay about how loaded your question was, the implicit assumptions in the way it was written, the way that "BIOLOGICAL" is implied to be a way to ignore social conditions, and the contempt for ""Gender Studies"". But I won't, it's very tiring and there will be 10 other people like you tomorrow.