As someone who's been in a very long lasting relationship you can easily tell which girls you should or shouldn't say that line to.
Scenario #1:
you know this girls life is makeup and she is a intermediate / pro. By looking at her face you can see she has several layers of makeup and this shows definition you otherwise cannot achieve naturally. It's best to avoid saying this girl looks better natural because she is as far away from natural as possible so unless you're good friends how do you know what she looks like natural?
Scenario #2:
this girl only has minimal stuff on like eye liner or lipstick, maybe trying to hide a zit or two but the rest you can tell is all her. You can complement this girls natural look anytime anywhere and are basically guaranteed a positive response as long as you're not creepy.
It's usually one or the other and if you think paying attention to what makeup looks and feels like is lame then gl dude.