Interesting question, and indeed answers.
If I may interlope and digress for a moment, in one way of course I can't answer this, because I'm so far down the track that if I woke up with amnesia all I'd see was a mature woman who has been unambiguously a woman for almost all of her adult life and thus there is no conflict.
However – going back to early life when my genitalia were different, it was simply the fact that my genitalia never felt physically "right" to me. I can't exactly describe it, because it wasn't pain, and indeed though there was some very minor malformation, it wasn't really that extensive or significant. I was only partially androgen insensitive, so it wasn't gross deformation either.
I'm not that bothered about all the gender stuff, I don't do makeup or all the girly frippery. However I'm actually quite feminine in my habits and personality. I've been a mother, and as my fellow students would tell you, I'm often the sympathetic ear, with the hot mug of homemade soup to comfort the weary. I'm also happy with a lot of the masculine attributes that I have, like slightly larger frame size, and more powerful voice, and I have always used them to good advantage. I admit that it may have helped a little that none of my attributes was ever really outside of the potential female range so I never had issues with being misgendered, but in the end it still boils down to the simple fact that I just didn't feel right having a penis. There was nothing else wrong.
Bloody good job I was never subjected to your fabled standards of care tests because how could I have meaningfully "transitioned" or done an RLE, when I was already the person I am, in pretty much all but my genitals?
Point is, from the age of five I was allowed to I grow up as me – and so there wasn't any real dissonance, beyond the genital one, and that was the only thing I have sought to correct. Yes I take HRT, and yes I had genital surgery around 30 years ago. The rest of me was, and remains, very much business as usual.
Now I have to say that I am fascinated by Trans people because I kind of feel that I came so close to being one, but somehow dodged the bullet, so that I can't ever fully comprehend what it feels like.
When I qualify as a doctor I wont be treating gender patients because I don't trust myself to be sufficiently objective, but I am fascinated by the more general idea that in some way important aspects of our identity may be hardwired into our brains, before anything happens to us, as indeed mine seemed to be.
... and now I must return to my study of Anatomy and enervation - which penning this reply has proved an enjoyable diversion from.
I shall read your further answers, from my seat in at the edge of the field, with fascination, and thank you for sharing.