Biology and medicine are not like physics and chemistry.
Take gravity for example, our equations and constants for gravity are mathematical representations of an observable force that is a part of the universe. Gravity never changes. If there is an anomaly, it means we got something wrong and need to go back, check everything, and redefine everything.
Biology is not like that. DNA is always mutating, its the fundamental phenomenon behind evolution. Definitions in Biology and medicine are largely based around typical vs atypical. How many fingers does a human have? 10 right? but some people have 12, some have 11, some have 9. We dont consider humans as having about 10 give or take a few, we consider humans as having 10 fingers because thats the typical number of fingers to have. There exist those who have 12 or 9, but they are atypical, and are not considered to be representative of the norm.
In the same way, yes there are genetic disorders that result in people having xxy or yy, or those who have genitalia that does not match their chromosomes. But these are disorders, they are atypical, they are outliers and are not representative of the typical. For the typical, chromosomes are in fact indicative of sex, and their genitalia match their chromosomes. Thats why the 0.1% is not significant in regards to the definition of sex.
As for the show, it is absolutely not a "science show" its an opinion show that masquerades as a science show. And I'm saying this as someone who agrees with its opinion a majority of the time. Lets look at the first episode. I believe climate change is fueled by human activity and is a massive problem that will kill us if we don't solve. That being said, the episode on global warming was awful. The "science" in the show was absolutely awful, it was him blowing bubbles and boiling water, and btw, why was he even using the boiling water to begin with when sea levels are rising not because the water is expanding due to heat but because the ice caps are melting as a result of the climate changing. This kind of garbage is not a science show, its just Bill Nye sharing his opinions, and saying "this is what the science says" without ever bothering to actually explain the science.
As for redacting the statement on chromosomes being indicative of sex. The general scientific consensus is that chromosomes indicate sex, it hasnt changed, nothing happened since the show aired that would justify removing that statement as an integrity move. There are no new arguments, no new statistics, the science didn't change, their opinion did.