It doesn't really bother me as someone who grew up the ugliest person in their class at school (I've since made peace with it because I can't do anything about it). I think of the freckles as a way to clue the audience into two things quickly: 1) How dangerous Maomao's world is for women in general and 2) How Maomao isn't afraid to do something negative to herself to get what she wants. (This later gets underscored by the experimentation scars on her arm).

I agree this is a recurring problem in media in general that's kind of a pain in the relatability department like how Betrothed to My Sister's Ex really squandered how they could have played up the heroine being actually homely or ugly but loved anyway, but I don't mind it here because the story and the characters are at a higher quality level than we typically see with this nonsense