Of course, there are other legal limits on dress codes. You may be protected if, for example, you follow a religion that prohibits cosmetics or have a medical condition that restricts you to flats.
But mounting a legal defense at this stage seems premature. It's not clear that your boss's "should" means you'll be held back or fired if you don't trowel on the face spackle.
Your first step is to make sure you're already meeting your employer's written standards for attire and grooming. You can add non-gender-specific polish with crisp, conservative tailoring and pristine accessories (glasses, shoes, laptop bag) - no wrinkles, scuffs or fraying.
If your boss continues to hound you, you can ask - as neutrally as possible - why she thinks makeup and heels are necessary for you. (I for one would love to hear how a dewy complexion, moist lips, shapely calves and uplifted buttocks are essential to your job.)
Finally, you can explain that you find makeup and high heels so uncomfortable and distracting that wearing them will hinder your performance.
Meanwhile, gender norms continue evolving. Just as we now scoff at the notions that women's trousers are "unprofessional" and "real men" can't rock long locks, perhaps we'll someday conclude that any women-only makeup mandate is - as a lawyer might say - discriminatory on its face.