Binary is a number system, nature does not use numbers, they are too clumsy and ill defined and binary is the clumsiest off the lot
It's binary because there are 2 sexes required to make a new human. Not because every human exactly fits into one of those two boxes (although the vast, vast majority do, and those who don't are usually sterile due to their chromosomal disorder - note, still valid, real, humans - just not part of the reproductive binary)
The existence of people who are XXY (or any other makeup) doesn't negate that.
Also, your chromosomes don't change. If you're born XY, ie male, you can never become XX, ie female.
If you are born XXY (I believe defined as an intersex male) you can never become XX or XY.
none of these are value judgements, they're descriptions of reality.