"SHE doesn't understand what's make up is in the adult world, it's just pretty, glittery colours to her to dress up in"
I don't apper to understand what make should be about "in the adult world" to me and my 28 & 18 year old it is glittery colours and part of the enjoyment of putting together an outfit (my 16 year old is a Goth with blue hair, so body adornment is used to be part of that sub culture).
If the youngest is only 2, then has their Dad moved into your house, with you and your children? The focus should be on making the girls feel welcomed and accepted when they come to stay.
Their Dad should be getting to know them as individuals and if then he thinks any interests don't come from a "good place", he should be trying to correct that, slowly.
They will change throughout growing up and he should respect them developing as young women and not reading into what isn't there, applying colour to any part if the body for many, is just fun and nothing more.
Personally I don't get the connection between using something which is a cultural norm and in every shop, or removing body hair (another topic on this board) as being connected to Morals or Self Esteem, necessarliy.
It's good that you are asking on here, it helps to remove preconceived opinions and realise that we all think differently.