...How did intersex come to be allied to others who are a part of LGBTQ activism and community? Homophobia is the simple answer. Although people with physical differences are often subjected to prejudice because of those differences, for intersex there is more to it. Intersex researchers have noted the most common concern for parents when told their child is intersex is that it means their child is gay. Intersex surgery on infants addresses those parental fears by modifying anatomies so children will become men or women in heterosexual relationships.Many intersex, on learning of their differences as adults, are rejected by their partners because of homophobic notions that their partner is not 'really a man/woman'. Others are pressured to undertake masculinising or feminising medical treatments and surgery so they are clearly seen to be the 'opposite' sex of their partner lest the relationship be thought of as somehow 'gay'.
Although generalised revulsion against physical differences may account for some of the prejudice, the driver is fears held by many that if the sex of a person is uncertain then the nature of that person's sexual relationships is uncertain.
Intersex people are not part of LGBTIQ because of sexual orientation or gender identity. All of us in that alliance are bound by the nature of our oppression - homophobia.
And, I would add to this the argument I've made in the past regarding homophobia: homophobia is in large part rooted in hate by some of any expression of gender that deviates from societal sex and gender norms.