I think you are wrong and possibly overthinking it.
Traditionally when talking about sex you say male and female. And most of the population have grown up with that.
And the fact that they ask both about sex and gender will maybe for some mean it is the first time they have though about it.
Personally I think they should have asked do you have a gender identity. If yes which?
Also, I suspect it is in line with census question, which is usually the basis for asking questions like this to compare to census stats.
And as we know from the census there is clear evidence that most people have no idea what gender identity means.