I'm probably repeating what I said back in that long 2022 thread, but I basically agree with you but have a few thoughts of my own to throw in. But to your four points:
1. I completely agree. I also personally think that the track list on the jackets Capital printed was the tracklist Brian was working with at least through January, and that Brian fully understood himself to be recording an album with those 12 tracks that would ultimately be pressed and distributed in those jackets. However, I've never seen any evidence from the period that suggested segregating each side by theme. I'd be very interested to be proven wrong on that. But I think it's just as likely that the two themes would have intertwined (sometimes within songs, even).
Yeah, it just makes sense. I know Brian said years later he'd never seen it before but frankly Brian says a lot of things that contradict and by the '80s or '90s I think he went out of his way to shut down or obfuscate attempts at clearing up the SMiLE mysteries. Considering the biggest missing pieces from the tracklist are Holidays, which I'm certain was junked, and I Ran, which may well have been too, it seems intuitive. If Holidays were there but something major like Worms or Wonderful wasn't, then I'd be more inclined to say the tracklist was wrong.
EDIT: Forgot to reply to your thoughts on "my" groupings! So there's no hard evidence for this, just intuition. As I'd said a lot back in '15, WC/W/CIFOTM/SU all have really prominent pianos and horns as well as a more somber mood and lyrics about children, innocence or the passage of time. Even WC, which admittedly is more of a stretch, has "in the late afternoon" and wind chimes traditionally were associated with death, but it's not a perfect fit and admittedly Brian was just writing about something he bought that day. Meanwhile H&V/VT/CE/DYLW are more connected in being explicitly Americana (Veggies as our breadbasket and I always saw it as an outgrowth of Barnyard as much as the elements, plus it absolutely fits tonally with Heroes as the two most upbeat tracks on the whole album). As for the question "why group it by thematic movements" I just think it sounds better, really. There is the quote from '03 saying "we ADDED a third movement" implying there were always two as well as another quote I unfortunately can't find again but recall where he said it was "originally a two movement cantata." Either way, everyone acknowledges the Americana thing and BWPS' second movement is basically everyone's favorite part, none could deny it works. I'm not saying it's definitely how it would've gone but there's at least as much evidence for this format as any other and, to me, it sounds good so that's how I do it.
2. I completely agree that The Elements was going to be a single song with four separately recorded sections, although I think it's more likely Brian would have used hard cuts than cross fades, as was his style generally. But I think it's also worth considering that at some point Brian either considered or decided to have just fire + rebuilding instead. I also think, in my personal opinion and personal read of the surviving evidence as I understand it, that people, in general, are too quick to jump from "this wasn't finished" to "Brian couldn't figure out how to finish this." The way the sessions went suggests, to me, that Brian's (foolhardy) attempt to turn Heroes and Villains into a followup to Good Vibrations, beginning in early 1967, led him to stop work on the other tracks and focus almost entirely on a new single for the remainder of the sessions. My take is that Brian didn't fail to complete the Elements because he couldn't figure out how, but rather because he stopped trying to complete anything on the album other than Heroes and Villains (and briefly Vegetables, when that was imagined as the new single).
I get what you're saying with "just because he didn't doesn't mean he couldn't." My intuition is/was he couldn't because it seemed plausible that focusing on Heroes occurred as a result of writer's block, plus the supposed mental block from "causing fires" might've killed his interest in even trying to. But it's not a hill I would die on to say "Brian couldn't finish the elements" as much as "he chose not to."
I will say, that if it was really a 4-part, abrupt-cut instrumental I don't know how he'd ever make it sound good, but maybe I'm projecting my lack of song-editing skill and compositional imagination onto him. I've tried various cuts of a single Elements track with Fire/Workshop/Water Chant/Breathing or Fire/Undersea Chant/Breathing-Smog snippets-Laughing and then going into Veggies and they sound...fine...but it's not something I'd have rubbing elbows with CE and SU if not out of faithfulness to the original concept for the album. I'd certainly love to hear what '66 Brian really would've come up with, of course!
4. This is an interesting theory, for sure. It feels intuitively plausible, to me. Although at risk of repeating myself, here too, I think that by early 1967 Brian was no longer recording in a way that really made a lot of sense if your goal was to finish an album, and that this, and not any particularly manifestation of the problem, was the key issue.
Thanks for keeping the Smile discussion alive!! I love it and always have

Thanks, glad to hear that, and my pleasure!