In addition to feeling (in my head) that my body was built like a female's and experiencing sex as if my outie was an innie, I also had other phantom symptoms:
Before I started HRT, for decades I would get very tender nipples, and aching deep inside where my vagina and uterus should have been, about once a month. It was sometimes pretty painful; the closest thing I've heard described was someone whose PMS included endometriosis.
That cycling went away when I started standard high dose HRT, but can start up if I miss a dose for very long.
It is theorized that transsexuality at the minimum is an intersex condition of the brain, but I suspect that for some of us it extends to other systems. I don't know if mine was/is all brain or something more.