I saw this again on Tuesday and kept an eye out for the body double. The actress posted a pic on her IMDB of the scene in question and I could believe it. The way they shot it, with her face partially obscured by the light and dark made sense and it did appear like it could be one. It's really the only scene in the entire movie apart from maybe the pool scene that could be a body double. Those are the only scenes where her face is obscured. I highly doubt the rest are anything but Eva green au natural, too many closeups and it's not too surprising about her being topless or even naked, she seemed to be naked at least once per penny dreadful episode.
As for the body double, maybe she's not comfortable with full on naked sex scenes or maybe she wasn't available for that particular scene.