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I've only played this and the immediately prior update, so small sample size, but the last update took Rachel from about the same place as the other girls who can be leveled are, and (I assume) finished her story arc.

I did not get the Emily scene on either playthrough. First time, I just explored, so didn't worry about getting everything, but second time, it was the only one I missed as well. I think you need to trigger the first scene with her already after passing Uniform Check (sounds like you did) then come back to her again right after you pass Confiscate.