Ok. But these are the exception and I believe (maybe wrongly) that they are a minority among the minorities.
They are not a minority. Plenty of people are not 'perfect' XY or XX.
XX male is generally 5 out of 100,000 births.
XXY can be as common as 1 out of every 500 male births, but it may not present in a way that many people even know they are XXY (most diagnosis comes in adulthood)
And they aren't what I would call exemptions. It's how biology works. It's not just two genders anywhere in nature. There are animals that can be both male and female, or start as female and grow into males, or the other way around. The rigidity of "born with dick = male, born with vagina = female" is a human social construct, not a biological one.
Are you saying men arent born men because of those thousand people?
Not sure what you mean by this. Of course if you are born male and identify as male, you are male. Technically, though, we all start as female in the womb and only become male while developing throughout pregnancy via androgens, which continues after birth until our puberty is complete. This is also why if someone reveals they are transgendered at a young age, we can actually postpone puberty so that transgendered persons can get enough time to receive treatment and grow into their actual identity.
ie, a transwoman can get treatment and hormones to grow breasts and avoid masculinization of her body. A transman can get testosterone treatments and grow up in a body closer to his actual male identity. Not everyone opts for bottom surgery, so a lot of times this is enough for them.