Judaism only seems to recognize Male and Female in the Torah, so aren't the concepts of non-binary and transgender against Jewish values?

In the bible, G-d is said to have created Zachar and Nekeyva (Feminine and Masculine energies). According to Kabballah, these are different energies that all beings have access to.
This is how we can go from a gender dichotomy to a non-binary spectrum. If everyone has different amounts of Zachar and Nekeyva, then there are actually infinite diverse possibilities of gender.
The Torah itself describes 6 different gender labels, Zachar, Nekeyva, Andregonis, TomTom, Saaris, and Aylanis.
Biblical and Halachic language about gender and sexuality are often physical descriptions, not identities. It is helpful not to confuse technical objectifying language with the way we refer to people.