Your argument seems to be that if the law accepts one backwards notion, that all the other ones should be expected to be accepted as well.

That's exactly what the law does presently. The law doesn't differentiate between one religion being less backwards than another but accepts them all as valid belief choices under the principle of freedom of religion.

Misogyny and racial discrimination aren't particularly different from religion or gender ideologies in what you said, and yet we have laws against them

And yet we don't have laws banning the concept of religion or the concept of gender outright. Also, the assumption that gender is inherently a harmful concept akin to misogyny or racial discrimination is a feminist ideological point, not an academic point. Academics on the other hand have long held the opinion that different societies around the globe have different gender norms, not all of which are to the detriment of women. For example, the fact that most societies expect women to become mothers and organize themselves around this expectation is not due to "misogyny" (as an anti-natalist feminist would argue) because at present most women do want to become women, even in Western countries where they have the option not to, so it makes sense for societies to expect most women to become mothers and to organize themselves anticipating that this gendered expectation will be the case for most females in that society.

Lastly I am not vaguely referring to a law in theory, I am referring to an actual legal precedent, one that is referred to in almost every subsequent trans rights related case:

https://www.aclu.org/legal-document/schroer-v-library-congress-decision

Go and read it for yourself. The judge compares a gender transition to someone changing their religion, and says that someone should be allowed to change their gender the same way someone is allowed to change their religion. The fact that both gender and relgion have no basis in reality is irrelevant to this judge.