I think "biological truth" is loaded here. In terms of a census there is an ambiguity about what it is that you're counting, are you counting people biologically born a given gender, people who are going to pair with the opposite sex, people who prefer a particular prefix or people that can give birth to children?

It appears in this case the census is content in counting people who prefer a particular prefix and only counting that (which can be self-identified) achieves its aims.

Tbh I don't massively see how this changes how one might treat census data (especially since the numbers remain small enough). I would suggest that if your research requires data points for people born as women then maybe you should be looking for other datasets such as births.