Time to address the issue and question some obvious scenarios! Transgender Studies. I found it very helpful. If she has fully transitioned, he may never know the difference. Which is why you can get XY women, and XX men.
Sex and Gender:
Identical twins have the same genes, so if gender identity were entirely due to genetics, you would expect that two identical twins would always have the same gender identity. Him hearing it does not make it real. Use neutral pronouns for everyone. This is why suicide rates are nearly as high after surgery as before surgery.
Many of the aforementioned traits or aspects of identity may have roots in certain genes that affect many parts of a person, and environment can certainly interact with genes.