I haven't been able to play Sun or Moon since I'm poor and I can't afford a 3DS (and yet I browse the Pokemon subreddit frequently for some reason...), but some people in that thread are saying that Lillie said the "male dialogue" to their female MC. Perhaps the line she says is determined by some other factor?
The author referenced the supposed "male" dialogue with the female protagonist, and the story is most likely based on the author own experiences with the game. There must be something else that determines this dialogue.
Hikari x Shirona (Dawn x Cynthia), and Elesa x Slyla were still going strong for a Pokemon pairing, but I'm glad Lillie and Female Protagonist brought a high dosage of yuri back into Pokemon. I hope we get to see more Lillie x Female Protagonist doujins in the future.
I too want more Lillie x Protagonist. I mostly work from pixiv/twitter, and I have a few more shorter things lined up, but if someone gets a hold of cute raws, email me at superidoltime@gmail.com and I can maybe make it work out.