While hardly a very common scenario, “Father of the Groom” doesn’t seem like a particularly wrong label in this case. She is the biological father of the groom. If circumstances of her gender identity have changed in the interim, it doesn’t change her original role and if it’s fine with her and her son, then anybody who remains confused by it can draw their own intuitive conclusions or discreetly consult with someone in attendance who is more familiar with the family history. In short, I’m not sure this is that much of a challenge to language as it may appear if people decide not to make it a distinction to be deliberately obtuse about.