It's hard to understand what kind of emptiness they were talking about. I can't remember a single moment where Fuuko was anything like that. I can't even say she and Mashiro are similar in any way. Regarding the eyes, maybe the author is trying to create symbolism in some finale where Fuuko is chosen and her eyes change. In general, knowing how Fuuko perceives everything except Yuni, this emptiness with Mashiro could be exactly that.
But for me, this whole flashback was very drawn-out and uninformative. I expect to see how Mashiro pervert Fuuko, but if that's all, I don't even know what to think.