“Variations neither injurious or useful aren’t affected by natural selection but would be left a fluctuating element”.
This is central to the discourse of intersex phenomenon from an evolutionary perspective.

The fitness of animal species entirely depends on its ability to propagate & produce progenies. The occasional sex anomalies/abnormalities are byproducts of mutations.
(side note: mutations are really an umbrella term that take many forms).

Mutations are the fuel of evolution. Only two fates exist for these mutations: they are either lost or become fixed in a population. If lost, they will no longer appear in the population. If fixed, they will constantly be reproduced.

By constant, I mean 50% of the time. Like flipping a coin because there are only two outcomes in question, this, the 50% chance. Until the variation is fixed/lost, they will fluctuate. The intersex phenomenon is a essentially a fluctuating mutation in the population.

Their condition arises from random, de novo mutations—mutations which are not present in the maternal/paternal genome. This happens all the time to even non-sex chromosomes but we will only focus on sex chromosomes for now.

So, the mutations that give rise to intersex people almost always result in infertility in which case natural selection cannot act on their genetic material that is not inherited or passed down to the next generation.

The key here is that genetic material must be heritable & passed on for natural selection to act. If it’s not passed, then there are no forces acting on it. No drift/selection/natural selection.

In the case where some intersex people are fertile & pass on their genetic material they do not pass on “intersex” as a sex chromosome but will only either give rise to female/male gametes. These gametes, upon fertilisation, will form either XX or XY sex determining chromosomes

This then lead to a normal sex development in the progeny as either fertile female or male. Intersex as a phenomenon is not passed onto the next generation. There is simply no “third sex” here.

Why then do intersex people IF FERTILE (rarely so) produce either fertile male or female progenies? That is because there’s a positive selection for the proprogation of female & male sexes determined by the XX & XY chromosomes.

The favourable variation that’s FIXED in the population always ends in a 50/50 chance of producing a male/female progeny through sexual reproduction. Anomalies do arise outside of the 50/50 chance through random mutations but they don’t materialise any further than that.

Anomalies are essentially fluctuating variations that are neither beneficial nor detrimental have no real affect & don't defy the established principles in human development.

This is especially the case when intersex individuals are infertile & don’t pass on their genetic material & even if they do in rare cases, they do not pass on intersex phenomenon.

Let’s contextualise this further through our phylogenetic position in the mammalian clade. Picture an evolutionary tree containing just the mammalian species (or mammals).

In the history of mammals which began ~200 million years where sexual reproduction strategy has been central to their existence & ours, no intersex phenomenon has become fixed in the population to give rise to three sexes. It is simply two gametes fusing to produce..

..either a male or female progeny. Our evolutionary history as humans may be young but our clade is a strong indicator of sexual reproduction strategy that favours male & female sex (XX & XY in humans)—a binary.

Complexities in development gives biologists work to do but it does not negate the fundamental principles. Evolution in mammals & in humans favour sex as binary because it ensures fitness. Fitness determines our continued existence.

How you masculinise or femininise these sexes through myriad of changes in appearance is a portrayal that you wish to communicate in a sociocultural way. But that sociocultural reality you create is not necessitated by biological sex (determined by chromosomes).

It took me halfway through my masters degree to properly understand gene expression (how genes are “activated”) & how that happens or the implications of it. Whilst genetics as a subfield is full of complexities which I’ve spent many years doing, I can say with certainty

there are fundamental principles that remain constant. So yes, almost all biological phenomena can be simply explained. The complexities are just an added layer in understanding the basic principles. But these complexities do not negate the principles.

My doctoral work centres on untangling these biological complexities. It is impossible to ask the right questions and truly understand anything without proper fundamentals. All these ambiguities I see from other "biologists" really stems from them not knowing the fundamentals.

Meaning, they don't understand how these complexities even relate to the principles. So the excuse "biology is too complex" or "we don't know anything" is often thrown around. This really reflects their poor understanding of the subject. Science is not the problem here.