You‘re right that people don‘t like the world to be too complex, and if something occurs with 1 percent frequency only, they tend to ignore it.
Speaking about intersex, which is what the links refer to, it‘s a biologically detectable mixture of the male and female sex, either on the level of chromosomes or hormonal functions or sometimes also genitals. The problem about the latter cases is that doctors like to play God and „correct“ ambiguous genitals in babies, and in some of these cases it later turns out that these persons have a different brain sex that doesn‘t match what the doctors did. So that‘s a big discussion now.
In Germany the highest court has ruled that a third gender be introduced in official documents for those who were born intersex and can‘t identify with either male or female. That is only true for a small minority, most intersex people do see themselves as either male or female. This all is ridiculed by a part of the population. Some, as you say, either don‘t change their thinking despite biological facts or indications, or they even deny that these facts exist.