Sexual orientation and gender identity can definitely overlap. That still doesn't change the reality that the mechanics of genitalia CAN BE a major factor in one's sexual fulfillment. Not for everybody, obviously -- but for many people.
There are gay and straight people (cisgender and transgender alike) who derive sexual pleasure beyond one's genitals. And then there are other gay people or straight people for whom genitalia is a central component (albeit certainly not the ONLY component) in attaining sexual pleasure. I fall into the latter group, and so do millions of others. I would imagine that there are far fewer transgender people than cisgender people who fall into that latter category, since cisgender people usually receive the privilege of automatically being acknowledged as the gender with which we identify.
I don't understand why our sexuality should be stigmatized when it isn't harming anyone. Just because somebody doesn't want to have sexual relations with another person (based on that person's body) DOESN'T mean we're going to close ourselves off from platonic friendships with them nor are we going to sit idly by while hate crimes are committed against them.