I know, I was wondering if I had to do the same thing for all free times or if I had to do something different
No, I think it should be only the third (even if their routes weren't there yet, their two dates were there in the early access, so I remember that). The other free times shouldn't matter.
From what I recall, depending on what you choose to do in the flower field that time, you'll get one of the Fae or the other, so I suppose that should unlock their route (which you have to choose at the end of the prologue, but I supposed you know that already)… I haven't played their routes yet, tough, so I can't check if it works for me. If you meet the Fae you're looking for in chapter three and still can't unlock their route, it'd be worth letting Crescence know :)