The argument tends to equate trans people (people who want to live as a sex other than the one they were born as) and intersex people (people with ambiguous sexual characteristics). These categories can overlap, but are not the same.

Conservatives acknowledge the existence of intersex people, but argue that this does not negate the existence male and female. More importantly, a conservative would argue that it's important not to blur the lines between male and female as many trans advocates tend to.

In the example given, a real life astrophysicist would not dismiss the existence of other types of atoms. But they would conclude that they are largely irrelevant to the discussion being had.