Well, one-fourth of one percent (0.25%) of 7.5 billion is nearly twenty million people, so no, I don't think that "standard human biology" should ignore the existence of those people.
More generally, I think that letting people understand that even if they're outliers, they are valid and there's nothing wrong with them is more important than...whatever benefit you derive (and I admit, I am unclear on what that is) from pretending intersex people don't exist.
Just read some stuff incidental to this thread, and I'll add to this with the information I have at hand (I agree with you and want to expand on it). It's a bit off kilter, but I think it's important: I'm going to talk about bees for a bit.
No I'm not going JP lobster on y'all, rather I'm going to use it to nuance a point about species. I'm also going to sound a bit mechanical and blunt about a number of different "deviant" groups in the human species, but only to dismiss how relevant the 1%, 0.1% or 0.01% point is. All of this "X% of the population is too little to matter" assumes that below a certain % of a species, something isn't part of it.
In a 50,000 population bee hive, which is common, exactly 0.002% of the population deviates as a queen. Her genetic makeup isn't fundamentally different, rather a queen can be forced to exist from any larvae through drones' injection of a particular substance whose name I forget (it's a bitter, milky-yellow liquid which contains a lot of different stuff; other than nutrients, it includes stuff like hormones, which shapes the end result of the larvae into a queen). Humans recognize the queen as part of this makeup because she's key to bee reproduction, but the point is that the number of a subpopulation of a species as deviation is never really that relevant, especially for a species as behaviorally and socially complicated as humans. To put it bluntly, the point of this whole post:
Evolution is weird, and species are weird.
Now you're talking about nipples and other small deviations, I'm going to bring up another point. Extreme conservatives bring up gay people, for example, particularly their lack of reproduction under a monogamous pairing of two gay individuals (let's ignore artificial insemination of lesbians for now, we're talking genetically). They argue for population growth and support this with the idea that everyone should form social bonds to reproduce because most people have the technical capacity for it. The logic is that as they don't have the ability to reproduce (they do, but let's go with it), they should be molded or controlled in order to rid our gene pool of it, it's not "human" enough to them.
In bees, IIRC the queen can lay up to 2.5 million eggs a year. The paper I read said something half a million, so we can lowball it at 500,000 (doesn't matter; point is, it's a lot for a single individual to reproduce). In humans, most of the population gives birth to only one kid at a time, and most females have the capacity for this. Twins, being about 3% chance, are still recognized as normal for humanity, although a deviation (kind of; not a deviation from humanity, but something expressed uncommonly in our gene pool). In bees, most of the individuals don't ever reproduce, but instead have a very practical function in the gene pool as to doing maintenance, defense and gathering nutrients. Male bees literally breed and die, which can be seen as nutrientially wasteful, why won't the genes let them just keep working after sex? This is evolution being weird in a sense, but bees were incredibly succesful until humans started screwing with natural fields.
If gay people can't reproduce (they can, but let's go with it), it's still not weird that they're as large a part of the gene pool as they are (~2.4% in the US), since there are innumerable other functions in human society that our genes might want. We don't bang all the time, and never have. Humans are not succesful because we are good at breeding. We are succesful because we're incredibly good at obtaining and maintaining nutrients after we become old enough to work/hunt/etc.
Back to the core point.
Having someone in your population that is gay, has a third nipple, is transsexual, has an anomalous chromosone setup, etc, doesn't make that person not part of the population. There is an incredibly numerous set of "deviations" from the conservative idea of gender and a standard body, and honestly, as long as the subject is "otherwise" "healthy", let them belong to the population and live their lives. The third nipple is useless afaik, but we're not arbiters of what evolution decided for our gene pool unless we literally want to go eugenic/genetic design.
The point is not to design our society according to bees*, but that evolution is weird, species are weird, and trying to draw borders of what does and doesn't exist in humans - when it exists in humans - is, to me, an unwelcome and alarming proposition.
Modern biology has found empirically out that human sex and gender is complicated, and honestly, I don't see why anyone would find it surprising seeing how absolutely bonkers our social structures can be - something that's actually an expression of genetics in a very concrete way.
* And JP's point about lobsters was that hierarchy exists outside humans, which is true, but missed the point everyone else makes that certain hierarchies aren't ideal. My argument is different, in that I think saying that the third nipple or intersex people aren't ideal leads us down a road I personally don't want to follow.
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And again, sorry about the bluntness here, but saying "deviation" and stuff is the kind of thing you're forced to do when faced with these points.