Thing is, There are less women in STEM, there are less women in management position etc. Therefor, either women are less interested/worse at these things (which is the conservative view) or society itself treats women differently than men. The rational behind affirmative action and programs geared towards women isn’t that women are less skilled and therefore need more help, rather that society makes it harder for a woman achieve the same as a similarly skilled man. By treating women differently we can help level the playing field.
Also, making gender “as unimportant as eye color in most things in life” is a completely unrealistic goal in the near future even in the most liberal countries in the world. We can (and do) strive to reach it, but that’s not a viable solution for issues we have right now.
And you know what? Legally changing your gender SHOULD be harder than filling a form. Someone who’s transgender should have no problem showing that’s what they are. The thing is to make sure the legal process is done respectfully, without making the person feel like they’re being interrogated.