it seems at least unlikely that an unconscious Spock (without the thruster) would travel all the way back, passing through the opening and closing doors (what are they for anyway?) ending up just in Kirk’s arms?
I always interpreted that as V'Ger having spit Spock out again via a tractor beam, after he became aware of him via the Mind Meld. It would have been better to show it, if that were the intent.
I think most people interpreted that thing as sphincter-like (cue the snickering). It could also be seen as a heart ventricle.
Even without the memory-wall, there's Fantastic Voyage analogues to be found.
I really agree that them going into V'Ger together and escaping together would have vastly, vastly improved the scene in sickbay where they hold hands. Plus, the sickbay scene could've been sped up, too, I think.
I happen to really like the hand-holding scene, in fact I think it's the linchpin of the whole movie, yes, even with Kirk acting stiff. It's hard to know what it would be like without it. You'd have to watch the whole thing through in an alternate cut, kind of like comparing the Donner cut of Superman II.