@ Nomura being cagey: I thought that he seemed ok with it all, until he started getting death threats and the like. Dismantled (Dismantling? I don't remember what it's called), memorial book thingie have always been on the pro-cloti side, haven't they? Or maybe they weren't. Maybe I'm making shit up or assuming things. Anyway, since the good ol' days of "Let's kill Nomura," he finally grew a pair, and isn't afraid of getting lynched by otakus anymore.
@ low affection scene, and why it's there: for the hell of it. It was there for the hell of it. Like Joss Whedon once said about the cheese man, some things don't have an explanation or a ~deep~ reason.
Also, the final FMV doesn't change, no matter which HW scene you get. You still get the two holding each other / hanging off of a ledge, and the two still seem to stay joined-at-the-hip no matter what.
Also x 2, in one of the interviews, didn't the 3Ns say that they had an answer for everything, but just decided to let fans "think for themselves" or some baloney? So, there is a ~true canon~, if you want to call it that... but if you want to think it a different way, go ahead. No skin off of their noses.