
Callisto only has 76% affection rate and he already asked her out, yet he did it mostly because it was the logical choice. Yes, there is some affection involved but the focus is the fact that they're two people shunned by the world. Why not stick together?
Penelope on the other hand realized that she is fond of him. She's at ease with him and I'm pretty sure preferred him over Eclis. It doesn't matter though, because just like Callisto, she's dictated by her logic and aware that the most efficient way of finishing the game is through Eclis.
It's honestly sad how love is just a means to an end to them. But I guess that's expected knowing that they hardly even experienced it. And the only form they know of it, isn't actually what love is.