Wow - a rant indeed. I cannot say I totally agree, nor do I totally disagree. Talk about sitting on the fence. Well no. As a Christian my belief is that man is man and woman is woman for a reason. As a lover of all things science I believe male is male and female is female for a reason. However, I TOTALLY get it when there's a genetic mix up somewhere. I have many transgender, gay and lesbian friends and I would not preach to them or expect them to be any other way as I expect that kind of respect from them. That said - I completely understand your concern for the welfare of the child. I have 3 stepchildren raised by a woman who birthed them then decided she preferred relationships with women. The children did indeed suffer at the hands of bullies and bigots and not just children they schooled with. Two of three grew up with additional issues of identity and sexuality, all are socially awkward, not sure where they fit in. Even as adults they don't know, and adults are more forgiving of these quirks and variations.
For a boy to be born of a mother who then becomes his father is like throwing a lamb to lions. Adults may treat him with respect but as he is growing and being nurtured his peers will be relentless in making sure he knows he is different. This may make him strong, come out fighting or weak and hide, but it will affect him in a way that will bite him. I guess without knowing the parent's strength of personality it's difficult to say how badly he will be affected but he will be.
In effect his mother has taken a perfectly ordinary boy (I presume) and made him a schoolyard freak and he will have to deal with that. Children are the cruellest of all, especially when someone is different for reasons they don't yet understand.
I wish them well and hope that he has the strength to survive without too much scarring.