Disorders of sexual development do not invalidate the sex binary, just as blindness does not invalidate the fact that humans are a sighted species. Intersex people are not a third sex; indeed the concept of intersex itself only makes sense within the existing binary - it literally means 'between two sexes'.
Imagine if we applied this logic - that disorders of development mean we can't make factual statements about standard human anatomy - to all of biology:
'human beings are a bipedal species'
That is not a biological fact. There are people born without legs and amputees.
'human beings have kidneys'
That is not a biological fact. Some people are born without kidneys.
FWIW, sexual dimorphism actually refers to differences in appearance between the sexes of a given species, especially size, e.g., some species of spider are highly sexually dimorphic, with the females many times larger than the males. I guess the more accurate phrase would be that human sexual reproduction is binary: disorders of sexual development exist, but there are no 'third sex' people who can bring a different sex chromosome (say, a Z) into the mix of the sexually reproducing XX and XY.