Calling it now, Lily totally knows the new Kaoru is a woman and is perfectly okay with it.
At this point "I knew all along" is becoming more cliche than "You lied to me". Like all tropes the execution is more important than the actual use, but it's not exactly subversive anymore.
This is exactly what I was trying to put into words.
“I knew all along” is cliché, and “You lied to me” is also cliché. Moral of the story: constructing an elaborate lie about who you are in order to fool your fated love interest is cliché and boring. Don’t do it! Be more interesting!