Okay...I'm confused again.
It seems there comes a time in every SJI arc where the questions pile up and you just have to let go, take each new page on its own, and enjoy the hotness of the moment; trusting that Daphne is going to make it all make sense in the end.
Even if it doesn't all make sense in the end. It won't completely because there's no way that a comic that's lasted this long will be completely consistent. (End? What end?) As long as enough of it makes sense I can just sit back and enjoy the ride.