Thanks for reading it. Skeletons of preadolescents are also ambiguous. More than that, biological sex is formed by more than chromosomes: a whole series of hormonal events take place to create it, and it can develop in some surprising ways (ie, androgen insensitivity: see https://medlineplus.gov/genetics/condition/androgen-insensitivity-syndrome/ ).
Bottom line: trans and intersex people's existence is as real and scientifically valid as cis people's: it's just a less common expression of human sex, like left-handedness (approximately 9% of the population), or blue-eyedness (8% of the population). Rare doesn't mean wrong. Somewhere around 0.05% (or maybe a little less) of babies are born with a full set of baby teeth. In the European middle ages, they would be seen as changelings or even demon spawn and probably killed. Fortunately, we've learned enough about biology to see that it's just a normal part of human variation. I hope it takes less than another 500 years for us to be as chill about sex and gender variation as well.