If you say yes to Kaylah (like I did in this playthrough) is that "her path" from then on? Because it sure seems like Charlotte path, but maybe that's just because the game hasn't progressed far enough to see the ramifications
IIRC there are four paths, one for each Lloyd woman. Kayla and Agent Fox are side girls who you can get lewd with regardless of which main path you are on, but doing so may or may not have repercussions with the Lloyd you are romancing.
In regards to Charlotte seemingly approving, this game is written so that the story conforms to the MC's choices. What I mean is, Charlotte doesn't start having serious thoughts considering being with the MC until AFTER the player chooses whether or not he is attracted to her. If he chooses to remain professional, her path doesn't start and she'll still slowly heal on her own but she won't be jonesing for the MC. Same with Lucy, at the scene where Lucy is carrying Charlotte back from the event where they have the first new incident with Jason, you can tell Lucy that she is worthy of love, but the real choice is at the end of the scene when you choose whether or not to say you will be waiting for her when your job guarding Emma is done. If you don't say that you aren't on her path and her internal monologue is disappointed you didn't choose her but is hopeful that you and Charlotte will get together.
With all that in mind, if you choose to be FWBs with Kayla, Charlotte will be supportive. But if you reject her, Charlotte is annoyed that Kayla even made the attempt. Her attitude is based on player choice, its a thing I've seen in AVNs a few times before as way to make it so that there aren't "wrong" choices, I think. Like the "where to cum" questions, whichever
you pick is what the LI screams out for, just on a more plot-wide scale.