The way I've heard it, Queen Victoria and the Church of England made makeup very taboo for men and women for a time because they considered it obscene. It was lavish and vain devilry, it was beguiling, sexually suggestive, and a host of other "negative" things, so misogyny dubbed it a feminine practice. And the idea that people in makeup were sinful and deviant stuck around better when the people in question were AMAB because once misogyny dubbed makeup exclusively feminine, the stigma associated with wearing it teamed up with homophobia and transphobia. But I feel like it's probably oversimplifying it all to say it's been shaped by a combination of "religious values." Namely the ones that aren't actually values at all, like misogyny and homophobia.