Yes, but more. Science also explains why there are two sexes (and not three or more), and also offers explanations to why not every component aligns 100% of the time. They are rare misalignment ("error" has negative connotations) from typical development following the mathematics of natural selection and reproductive success, whether genetic cases (e.g., XXY instead of XX or XY), physical development (e.g., hermaphrodites), different psychological gender identity (e.g., transgendered, non-binary), or even sexual orientation (e.g., homosexual, bi). Understanding why these cases occur, currently to varying levels, doesn't negate the underlying principle of binary sexes. Likewise, the existence of different types of colour blindness doesn't mean there aren't 3 primary visual colours. 

There's nothing morally wrong with any of the exceptions, and they have equal individual rights against discrimination, but nobody else can compel speech or ruin careers over individualized pronouns.