It will always be possible to highlight individual problems with data, there is no perfect measurement, no perfect analysis, no perfect evaluation; this is not in question.
There will always be a critique that highlights certain areas, a person that is motivated in one area, or another, to present an overall interpretation that bends to a certain perspective.
So what do you do then?
Do you take one person's critique for it (mine, or anyone else's here) ...or do you look for a broader analysis that has been arrived at by a collaborative of multiple experts in multiple fields and that is cited by governments and women's rights groups worldwide?
I'm not a conspiracy theorist, so I will do the latter. And I will trust that, broadly, a decent effort has been made to arrive at a measurement of, overall, how well women are doing are doing in different countries. And I will acknowledge that there are individual instances of problems, but this does not disrupt the overall big picture.
And the overall trend is this:...if you were to plot women's well-being and trans peoples well-being on different axes of a graph, and establish a scatter plot of corresponding data points on it, and then create a line of best fit through these points, you would clearly see an excellent correlation between the countries doing well for trans people and those doing well for women.