I think it is pretty clear that the interaction with Shadowheart on the Nautilus is only to set up her later dialogue with Charname at the temple entrance on the beach.
"I remember you, at least you tried to free me" etc.
"At least, you made the effort." Is a seperately voiced line; that means there's options for "You're the one who didn't even try" or "You got my pod unlocked so I could escape!". Not saying there *will* be of course, but it did leap out at me from the first time I played the EA. I've noticed there's lots of little things I'm not necessarily noticing either; Kanon and his sister, for example. There's now dialogue where she's kneeling over his corpse basically going "Please wake up!". I don't remember that being there last time either....