Let's create some thought experiments. Say God intends someone to be male. His conception happens normally. Oops! An extra X chromosome found her way in. Fortunately for that male and God, he grows up with Klinefelters appearing male as God wanted. Likewise, God intends a female who gets an extra X chromosome creating Triple X syndrome. She grows up looking like most females.

Now for some different situations. Then God intends to give parents one daughter and one son. Oops! The would-be daughter loses an X chromosome, giving her Turner syndrome. She'll appear female so God's happy. Her younger brother loses his Y chromosome which gives him Turner syndrome too. He too will look female like his sister. I suppose God's not happy. What do the parents and kids do? God didn't send the blueprint so they don't know if which is their "daughter" and which is their "son." Or maybe they're supposed to have two daughters or two sons. Too bad they each have only a 50/50 chance of pleasing God.

What if we combined gaining a chromosome with losing a chromosome? Since all the previous happen fairly frequently, (approximately: XXY 1 in 500; XXX 1 in 1000; XO 1 in 50),  it is inevitable that some would happen in the same person. In these cases we have an intended XY who loses their Y and gains an X. (The "opposite," XX to XY cannot happen because the additional chromosome must come through meiosis. Additionally, a YY fetus will result in miscarriage.)  That is, God intends a male but they end up female! So of the 3 billion XX females in the world, how do we know their true sex as God intended? We don't. Are all these females that God meant to be males sinning because they should live as men? Some of them (statistically, again) identify as men and want to live as men. If we honor God's intentions we should let them. Perhaps all transmen were really intended by God to be male and the Holy Spirit gives them the gift of discernment!

I hope this further demonstrates the absurdity of believing we have a true, mystical and invisible sex. The lesson here is humility. Let's not presume those aspects of God's intentions which God has not revealed through Scripture.