Ok so now I have played through all three version of the story I have created.
Version 1: Full Harem. By far the most enjoyable version. More content to see. Only saw one issue, a minor grammar error with words being swapped around.
Version 2: No Harem, Fiona only. Glaring inconsistencies with the story since Cecilia accuses the MC of sleeping with all the girls when he has done no such thing.
Version 3: Harem but only after Fiona came back and gave permission. Only missing one scene worth of content, the scene at the park with the doggo. Dont quite know why, I guess Tracy wasn't feeling as comfortable with Earth.
In conclusion, this was fun, you just need to be careful with dialogue and content that makes no sense when the players actions are taken into account.
Otherwise, you create the sense that the players actions actually have no meaning and then you should just remove the choices altogether and convert this story into a Kinetic Novel.
The solution I suggest is just to cut the scenes with Cecilia altogether when the player has chosen not to romance the other girls. You could rationalize it as Cecilia has noticed the MC is only interested in Fiona and thus figures she has no chance.
I would suggest writing an alternate scene where Cecilia asks the MC why he has refused all these lovely ladies, secretly trying to gauge her chances of succeeding where they failed, but thats more work and you likely dont want that.