Interestingly, the 1.7% of the world being intersex, which is where your >98% thing comes from, originated with the Sexing the Body book. Most of that 1.7% still have normal chromosomes, i.e., XX or XY. Only three of the ten conditions that she listed have abnormal chromosomes (Turner syndrome, Klinefelter syndrome, and other “non-XX or non-XY”), which in total make up 0.00193% of the population. So, in reality, 99.99807% of the population either has XX or XY chromosomes. From my understanding, if you use the looser classification of Y chromosome=male, no Y chromosome=female, you sex the person correctly about 99.9998% of the time (the only exception would be for a small subset of “true hermaphrodites,” where they have a Y chromosome but clearly have a much more female-oriented reproduction system).
And, yes, from the perspective of evolutionary biology, it makes no sense for there to be more than two sexes. There are only two types of gametes in the population, so a group that is either sterile or produces one of the two gametes cannot be a third sex. Colin Wright, if you’ve heard of him, wrote a paper explaining this recently https://link.springer.com/article/10.1007/s10508-025-03348-3