I think you misread the article. It is my understanding that the parties involved are:
1. Nicole Winstanley - a lesbian that was born (and still is) a biological woman.
2. Ronald Francis Terry (aka Barbara Lynn Terry) - a biological male that lives as a woman (i.e. wears dresses and makeup) but has NOT yet had his genitals surgically mutilated. He is still a man (no matter what he calls himself or wears), and the doctor testified as much.
Therefore one member of the couple has male DNA and the other has female DNA.
As the judge said, "Since Barbara Lynn Terry is a man under the law and has taken no steps to surgically become a woman, there is no legal impediment to marrying them. In sum, he is still a man and his bride a woman." The judge made the right call under the law.
Yep, I did misread the article, thought the doc had sliced and diced. Thanks for keeping me on the ball.