Earlier quoted context omitted.
In the context of there being measurable differences between the sets of males and females, 99% is binary enough.
"99% server uptime is enough!"
This seems analogous; we should design social structures (or allow social structures to emerge) that assume that individuals are male or female, but which handle the exceptional case of non-cisgendered individuals. Just like a software system that doesn't handle exceptions gracefully, a social system that lacks provisions for these is fundamentally flawed and can fail unexpectedly and potentially catastrophically.