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Heather may not have any foolproof evidence to back her statement, but there’s certainly a large number of factors that lend very strongly to her being able to suspect something is up with Rain. This discussion here, as well as her talks with Fara (back in Chapter 3) make it certainly plausible for her to actually piece this together. Plus, sometimes it helps to not really be directly involved with anything going on to see what’s really going on.
Kylie meanwhile, is the one hung up on this. I actually had his dialogue more or less lampshade my critics who always complain that “Rain passes too well”. I don’t get it myself (and I’d like to point out that many of those same people think this also assumed I was a genetic woman based on my picture!).
That said, if a reader can come to the unfounded conclusion that Rain is "too cute to be a boy", so too can a character.
Rain, all characters and all other aspects of the story are copyright material belonging to me.