Looking at your source hardly provides rock-solid evidence for your claim. Firstly, this was a tiny group of people (16)! And there wasn't even a uniform result within this group.
Sexual identity varied among the subjects assigned to female sex. Five persistently declared unwavering female identity. One other subject refused to discuss sexual identity with anyone. Eight declared unwavering male identity: four of these subjects declared male identity spontaneously, at the ages of 7, 9, 9, and 12 years, although the parents of two persistently rejected these declarations. Four others declared male identity after their parents revealed to them that their birth status was male, at ages 5, 7, 7, and 18 years. Two subjects were reared male and identified themselves as male.
But more importantly. Gender identity does not determine your sex.
Let me put this as clearly as I possibly can.
Classification into reproductive sex is based on reproductive systems.
That's all.
It's got nothing to do with brains. One's brain can identify however it wants, but that identity is irrelevant to how one's reproductive biology will work.
Unless one has an incredibly rare intersex condition, or medical issues like in the case you provided us, one's sex is observed to be unambiguously male or female at birth and remains this way.
If one was noted to have male genitalia and one developed normally (puberty, make sperm, etc), then there is almost no need to do a chromosomal test to check one's sex. It's a waste of time and money. Especially if one has actually impregnated someone.
If one is male, then one is male.
The doctor or midwife did not get it wrong. Even if one thinks one is female, deeply, inside, this does not make one female.
The biology one is born with, that reproductive anatomy, those organs, will always be the only relevant factor in determining sex. Not an internal feeling.
Now, is it possible that some people some kind of potentially neurological condition which causes them to feel alienated from their actual sex? Yes.
Is the concept of "gender identity" potentially useful to describe the predicaments of such people? Yes, but I don't think it's relevant to most people.
Is the current best treatment for intractable gender dysphoria to give cross-sex hormones and possible surgery? Yes, I believe so.
But those procedures do not change your sex!
And even if in the future we started brain-scanning people, and classify them as per some other “gender identity” system we would still have to come up with new words to describe reproductive sex differences! Plus, I would bet that the brain-scan version would have a higher rate of error than the system we have now!
In short:
I will concede that if there is a mismatch between one's experience of one's reproductive sex and one's physical body, then one can transition to make one's body appear more aligned with one's internal experience. One can become transsexual, but not erase one's birth sex entirely. One cannot claim one is exactly the same as the sex one "feels to be inside," if that is not how one was born. And one absolutely cannot "retcon" this and pretend one was "always" one's desired sex.
A better analogy is asking whether gender identity is in any way a similar "disconnection" experience as sufferers of Body Integrity Identity Disorder have. Those individuals also have an internal sense of their own body which doesn't align with their physical selves, and this can be incredibly persistent, with a huge amount of co-morbidity and distress. I've heard stories where sufferers have deliberately injured themselves in order to try and provoke an amputation of the "alien" limb.
When a person’s idea of how they should look does not match their actual physical form, it can be caused by Body Integrity Identity Disorder. This condition affects a small percentage of the population and is commonly manifested by a desire to have an amputation of a specific body part. In most cases, the limb that the person would like to remove is actually in healthy working order and there are no physical problems with it.
Many psychologists and neurologists have ventured theories into what causes this type of thought. The common leading idea is that Body Integrity Identity Disorder, or BIID, occurs when the brain is not able to provide an accurate plan of the body. In this case, the brain sees the offending limb as being foreign and not actually a part of the person, thus the desire to have it removed.
www.biid.org/