How can this kid even be considered trans? You can't be in the wrong body one day and in the right body the next!
If anything, he sounds like a gender nonconforming kid. In a religious school. Which probably is far more accepting of gender stereotypes than a non-religious school. Maybe his natural non-conformity is being shoehorned into a trans-identity as that's more acceptable to his (presumably religious) parents? He is six years old, right?
I suspect, once again, gender non-conformity, non-binary and transgender are all getting confused.
But let's say the kid was transgender. Is he going to be told in biology lessons that he can get pregnant? If not, why not?
Or will he be attending the lessons which advises him on how he might get someone of the opposite sex pregnant? How's that gonna go down? You're a girl, right up until the point, when you're obviously not.
Will the teachers be sent on a disciplinary course, because they are teaching this boy about his male biology. Or will they be told that that's fine, but all the children in the class have to pretend or they will be disciplined.
That's the trouble with a belief system.