If you don't mind, I'm going to repost the reply I left for another individual who brought up the same point to you.

I wouldn't say they are that rare. For the first syndrome, the article says:

This syndrome occurs in approximately four or five in 100,000 individuals

With over 300 million people in the United States, what is that, roughly 15000 people who might be affected by just that syndrome alone.

For klinefelter, the article states:

Klinefelter syndrome is the most common chromosomal disorder, and it occurs in 1:500 to 1:1000 live male births.

In my opinion, that's a lot more people than it sounds.

And then there's the case of individuals being born intersex (<-that article is an interesting read by the way). In these situations, doctors usually, or at least they used to, choose the gender for them based on what they have more of to work with. It's a very controversial and morally ambiguous topic for sure. We just don't know all the answers yet.

Now I'm no doctor or scientist, but unless we do chromosome analysis testing on every individual who chooses to transition to the opposite gender, who is to say they don't suffer from some kind of chromosome syndrome?

edit: I'd also like to add this last article about david reimer for further reading. Pretty much, this doctor preached the idea that gender identity developed primarily as a result of social learning from early childhood and that it could be changed with the appropriate behavioral interventions. His experiments lead to the suicide of both of his early test subjects later in life. His flawed reports lead to thousands of unnecessary sex reassignment surgeries.