and you can tell with the naked eye that an intersex baby is intersex, and neither "properly" male or female. except when the baby looks very female but is genetically male due to androgen insensitivity syndrome. then you need that microscope again...

kindergarten level logic fails at physiological sex ambiguity.

and it fails even more so at gender identity issues.

Not following your point, unless it's merely to say that parsing observable reality isn't good enough to determine the precise levels of hormones flowing through someone's body, which, fine. That's certainly true. However ... physiological characteristics are in fact dictated to a large extent by hormones, and as a result one can realistically make a good inference about e.g. who has more testosterone.