If not, how should I raise my concerns with my boss? I was hired for my research and presentation skills, but the makeup/heels requirement makes me feel like I was hired to look pretty.
As discussed before, employers have the right to impose dress codes and set standards of formality. But a dress code can't impose an unequal burden on workers because of their sex, faith, race or other protected status under Title VII. What's more, the U.S. Supreme Court in 1989 interpreted Title VII to prevent "sex stereotyping" after a company refused to promote a woman to partner because she didn't act or look "feminine" enough.
Then again, a federal appeals court in 2006 upheld a casino dress code that required female employees to wear makeup and style their hair. That court said dress codes can allow for "reasonable" gender-based distinctions and said the plaintiff had failed to prove the makeup mandate imposed an "unequal burden" on female employees.
Thus, gendered dress codes aren't necessarily considered discriminatory in and of themselves; such a ruling depends on the facts, the evidence and the court involved.
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.