I think the key point here is “The acceptance of our bodies as God’s gift is vital for welcoming and accepting the entire world as a gift from the Father and our common home”.
Surely that implies acceptance of our bodies as they are ,, recognizing that “body” includes both our physical and mental make-up? It follows that we should not be forced into arbitrary patterns of behaviour in our relationships or gender expression based on conforming to the standard heterosexual and gender binary stereotypes.
Further, as Peter Nixon notes in the comments you quoted yesterday, “acceptance of our bodies” does not imply acceptance of medically treatable pathological conditions. If the “body” someone has been given presents a dysjunction between its physical and mental manifestation, and that dysjunction is medically diagnosed as problematic, then acceptance of the body does not exclude medical interventions to rectify the problem.