Just beat Chapter 12:
Unfortunately, I got spoiled that Elma had a "true form" by accidentally clicking a spoiler tag. That said, I don't think I 100% expected her to be a xeno. I did notice when she talked about humanity she phrased her words in a way that hinted she wasn't actually part of humanity. I did wonder how people learned about the coming battle that would destroy Earth so Elma warning them makes sense. I'm glad we can switch between Elma's forms.
On to the post-game!
Chap.12 spoilers:
That Elma is an alien is heavily implied during the whole game. I wasn't spoiled but guessed that at around ch. 5 I think.
And yeah, I do hope we get a sequel.
My main complain with the game is the story. Not that I mind it is pretty light, it's rather that they raise an incredible amount of questions they simply don't answer. They really should've marketed the game as a prologue imo, all that would have bothered me less then.