This must be stressful and upsetting for both your relative and the family. So much so that you reached out here! I hope that despite the initially frosty reception you find what you need.
I agree with previous posters that your first port of call should be the school. They must understand that his condition has nothing to do with trans issues but is a completely unrelated medical disorder, a kind of disability for want of a better word.
Every school has certain obligations when it comes to dealing with pupils who have medical conditions. But I know from a friend of mine that sometimes no matter how hard you try, they simply do not understand rare conditions. All you can do is keep on talking to them and not give up. You must stress (even though this shouldn't be necessary) that he is unequivocally male, genetically male, brought up as male and not identifying as a girl so the school should not disrespect him by equivocating his condition with transgender issues.
Seeing as he is in his early teens, I think it is time to try and find a support group (I do realise that this may be difficult given the rarity of his condition). If there are none dedicated to his condition or to a cluster of similar conditions, it may be worth asking if intersex organisations know of a suitable support group - if you tell them that you know this is not an intersex condition but that you were hoping that they might be able to point you in the right direction it is unlikely that they will mind.
I have approached support groups myself before not being entirely sure if they were the right one for the issue at hand and have never had a negative reaction to that. And a few times they were actually very helpful in directing me accordingly.
A support group or even just a network of families in a similar situation can be very helpful. Sometimes just talking to another family whose child is older is incredibly reassuring (and often informative at the very least on what might be best avoided). The next few years will be tricky to navigate and knowing you are not alone is a comfort to many who suffer from particular conditions. Even if he - as you say - is not himself mature enough for a support group and may not be for some time to come, the family may find this beneficial in the long run.
Also, I can only agree with the others that the young female in question overstepped a number of boundaries. This may have been a deliberate barb or an unthinking remark or a heartfelt if misguided kindness. Nonetheless, she will need to be told that this was offensive and why.
And last but not least, if you haven't already, some form of counselling may be appropriate going forwards. Either for him and for him and the family. This won't get easier for a while, and the transgender debate is here to stay for some time, too, so he needs armour and tools to deal with this.