It's estimated (order of magnitude) at about 1/1000, or so. That's hardly "statistically irrelevant" - it means, for example,  that you'd expect a few dozen such individuals to pass through a busy airport like Pearson every day. And yes, not trampling on their rights means having an option like "X" so they're not pigeonholed into non-representative categories. 

Biological sex - meaning genitals at birth - doesn't necesssarily seem a useful identifying feature. Perhaps it was a hundred years ago,  but ipso-facto from 1880, does not mean valid today.