...you don't know how these things work or why they happen. Neither do I
Perhaps one day this will be explained scientifically.
I'm with you on the 'not knowing all about embryology' front
But there are people who do know all about embryology and genetics and human physiology - people who have studied those areas for decades, who have recognised qualifications, who have published in proper, verifiable, peer-reviewed publications.
It seems to me that the most sensible and workable way of seeing and understanding the world around us is to look at what is verifiable and verified in a way that is acceptable to most reasonable people, and go along with the best possible explanations. The alternative is constant 'what ifs' and getting information from less well informed sources. That's not very practical - the real world has to function on reality as currently understood.
The best possible understanding of human sex is that it is binary - you are either male or female, and even if you have a medical condition called a DSD, you'll have either a male one, or a female one - and immutable - your sex is encoded in every cell of your body, and even millennia after you die, some future Alice Roberts can look at your skeleton and say 'This was a female...'.
Even if they only have a fragment, they can test the DNA and say 'This was a female...'
It's an interesting intellectual exercise to speculate about 'Perhaps one day', but a 4 year boy who thinks he is a girl deserves the truth, not intellectual speculation.
Reality is going to catch up with that little 4-year-old. It already has.
He is going to learn that he can never be a girl, he can never grow up to be a woman, because that's impossible. He is going to be adrift in a world where outside of a certain bubble, he will always be recognised as male not female.
He may never accept that fact.
He may spend the rest of his life arguing against reality, medicating against reality, undergoing surgery and subsequent ongoing care against reality.
That's a big load to put on little 4-year-old shoulders.
Gender-confused children deserve love, support and above all, the truth.