Okay I think I've figured out how to solve the problem with the option to apply make up or not.
If you have Chloe study and I also had her dance a few times before taking the bath, the option has always appeared so far so I assume you just have to waste some time before taking the bath so it would make her late if she puts on the make up.
Edit: Well it worked for 1 week and then the next week the option isn't appearing again, man this is a tough one to figure out.
We really need a walkthrough for this.