Refusing to submit to an ideology you consider false is not withholding respect and dignity from anyone.
Your concept of 'submit' is rather strange. In any case, the school appears unwilling to submit to the teachers ideology, so you...support their position?
For example, I truly believe that all of Mankind are the children of God which would makes us spiritual brothers and sisters.
In my religion we refer to each other as Brother or Sister "Last name".
Could I demand that everyone I meet refer to me as Brother John?
You could, of course.
Keep in mind, that referring to me as Brother John would cause you to operate under my beliefs concerning our spiritual relationship.
Rubbish.
I still would refer to Imans or Priests by their honorifics. This is purely a show of respect, and in no way effects my lack of belief in their God's.
You believe that I should be able to force people to refer to me thusly?
Force people to use a title when they talk about you in a secular school?
No.
I would suppose you might be able to in a religious school operating beneath the auspices of your religion though.
If they don't refer to me as Brother John, I could claim they aren't treating me with respect and dignity and I could get them fired?
Of course you could claim it. People would think you're an arse, I would suspect.
The idea that a person can change their sex is just as religious as my beliefs concerning the spirits of Man.
No one is asking you to agree with sex change or anything else.
Indeed, I don't even know where I stand on every aspect of this.
But that doesn't matter. If the kid wants to be called a certain name, the parents are agreeable, and it's not causing harm to anyone, then so be it. Assessing the kids rationale is beyond the teachers expertise or role.
They are letting their religious beliefs impact on how they treat the child, and that is not appropriate in a secular school. That's it. The rest is window dressing.