I work for a medium-sized software company, we take diversity pretty seriously (at least, we seem to have a diverse workforce in engineering), and I don't think I've even seen any woman candidate for any position in engineering ever discriminated against for wearing/not wearing heels or make-up. Personally in my experience flats have been more common among almost all of the women I've interviewed for engineering positions. Most women candidates who I've interviewed and who were eventually hired had about the same amount of make-up that they ended up wearing once they've become a regular employee, at least it's never been something that I've thought about or seen other people consider in the interviewing process.
Of course, people could have their own biases that go unseen or unnoticed by me, too. I've definitely never witnessed anybody looking down on a woman candidate who did or didn't wear make-up or heels. FWIW, I don't think I've ever interviewed a candidate who wore anything longer than short heels or small lifts, maybe a "kitten heel," but honestly, thinking about it I think just about every woman I've interviewed has worn flats or an adjacent style.