Damn, that's kind of wild. It's very rare for a shoujo manga character development to be "actually you're not fine just the way you are, wear some makeup", as well as having the person saying that the one who's supposed to be "wrong" (the saintess's words that are commonly called empty/lacking thought).
I will say though that I like freckles and as much as I like character development, I hate to see em go.
It's definitely a choice.
A good faith reading would be: Society is pretty fucked, woman are expected to cater to men, even by other women, even if they aren't attracted to men. Jane let her resistance of said system turn into a complex, once she found someone that validated her in a way she always wished to be validated in, she became obsessed.
Now that she realized that, while not her mother, she had turned into someone just as bad. She now has to reconcile who she actually is with someone she can actually proud of being.
Her wearing makeup to try start loving herself more, is her first step to loving herself without the makeup and embracing her femininity.
A worst faith reading would be:
-wear make up women, you guys know that you are ugly without it
-Jane cured of being a lesbian now
-Freckles are ugly and you should be ashamed of them
-etc.
While I don't think it's as bad as the worst faith reading and I like to belive the author tried to go for the former, but this does feel like, whenever someone brings up how toxic our culture around make up is and the health problems it brings both mentally and physically and without fail someone just has to chime in "Well some women feel empowered by make up🤪🤓"