I think it's very possible she has a standard template she uses for pupils which will refer to they/them, rather than he/him & she/her to avoid having to change the email for each student.
I don't really think this is meant to suggest your dd is non-binary.
I couldn't quite tell from the OP whether the emails about OP's DD are specifically about her child or general class communications; but there's obviously a clash between those who accept 'they' as a neutral pronoun and those who believe it to be inappropriate and dismissive when referring to a single known person, whose sex/pronouns are known.
I always remember my DM telling me about the funeral of a Great Aunt that she went to, where the vicar continually referred to her as 'he' and 'him' throughout. Presumably, he had an old-fashioned standard funeral service sheet, using 'he' as the default, and he had neither the wit nor the basic decency to amend the pronouns accordingly when the service was for a female. The family obviously found this very upsetting and said it really spoilt for them what was supposed to be a very special day dedicated to remembering a loved family member, but where it seemed that even something as basic as her sex had already been forgotten.
Would it have been better if the vicar had just used 'they' throughout? Not much, I don't think: it would have avoided wrongly implying that she had been male, but would still have seriously detracted from her important, respected place in the family as a daughter, sister, wife, mother, aunt, grandmother - roles which are explicitly taken by females, who are thus referred to as 'she'. He might as well have saved even more time by not bothering to use her actual name and just referred to her as 'Jane Doe' (or, going on his record, probably 'John Doe').
Pronouns matter to us, and they're part of our identity - not just for trans/NB people, but for everybody. 'They' is appropriate if you're talking about an unknown/little-known or theoretical individual, but not when you do know the person very well.
A stranger walking past the playground might see OP's DD heading indoors and quite reasonably comment "That girl has left her bag on the bench"; but would you really find it acceptable or 'neutral' if the teacher, when emailing OP about her DD's progress, kept referring to her as 'that/this girl'?