I don't think there's much mystery behind the use of Smile tracks on 20/20. And although Brian consented, he was reluctant about their inclusion and hands-off with it.
Not speculative, Dennis went on record saying that they had to go back and find things Brian had left behind because he'd stopped actively participating. The sessions for 20/20 began with a Brian-led run of sessions for almost an a full album of songs in the summer, but most of those weren't completed, and activity drifted for months between touring until the group were facing an imminent delivery deadline. In September a lengthy list of potential songs for the album was drawn up (probably by Carl and Dennis) with notes on their status - some recorded that needed work, some originals that hadn't yet been taken into the studio, some ideas for covers, and some older tracks from the vault - with almost all of Brian's tracks from the May-July '68 sessions given a look, along with Iron Horse, Surf's Up, and Cool Water.
It was probably easier, and more comfortable at this point, for the rest of the band to record newer material rather than finish off Brian's recent work on his behalf when he didn't want to go back to it, which is where I Can Hear Music, Bluebirds and most of the Dennis songs enter the picture. But the Smile tracks were a looming exception that they knew the value of and had wanted to finish, with Brian alluding to some group argument that year over his refusal to use the material while he was still taking a more active leadership role. Prayer was already effectively done and only sweetened while Cabin Essence was close enough that Carl could add the finishing touches without stepping on Brian's toes. Considering they were in the last week of a tight deadline and looking for some strong Brian contributions that could be completed without too much work, those were obvious candidates.
Other parts of Smile were still in the air in '68. David Anderle got wind that Child is Father of the Man would be on Brian's next album, which ended up happening via Little Bird. My Only Sunshine and the original version of Wonderful were reviewed with Stack-O-Tracks material in January. Workshop, Our Prayer and Cabin Essence were used on 20/20, while the original Wind Chimes was also given a safety copy and Surf's Up was evidently still hanging in the background.
All interesting, but it really doesn't explain how the tracks went from being set aside in summer '67 to moving slowly under the band's control, especially since the band was at least part of the reason why the original material was set aside. The question that still needs to be answered is what happened to change around the notion that Engemann documented about a "10-track SMiLE LP" and what happened to Brother Records (since it was supposed to be a label for band members to sign other artists and, theoretically at least, work on solo projects).
The impression one gets from your wording is that Carl and Dennis were doing some kind of back-door advocacy for those tracks during '68. Up to this point the BBs had only released two significantly different versions of a song on one occasion ("Help Me Rhonda"). Brian had re-appropriated a few melodies in other released recordings ("Thinking 'Bout You Baby" and "Darlin'", and "Car Crazy Cutie" and "Pamela Jean") but those were for "other artists." Of course, a "10-track SMiLE LP" along the lines of what Engemann thought he'd be getting would have to use some of those original SMiLE recordings that were reworked for SMILEY SMILE, so some redundancy would have occurred that way.
I'm afraid we still don't know what the actual dynamic was about this material as it moved from July '67 through to the decision in the fall of '68 to grab two of the unreleased tracks for 20/20. The first question that might come to mind for followers of the various SMiLE tales is how Mike's objections to "Cabinessence" were gotten around. Has anyone ever had the chutzpah to ask Mike about the circumstances behind it winding up as an official release at that time? Inquiring minds want to know...
As Liz speculated earlier, the Redwood incident may have kiboshed any ideas that Brian had about going on with any kind of outside project. As it was in October '67, he had his hands full getting WILD HONEY together: the band had made it clear that they needed a new LP right away since SMILEY was floundering and there was no track on it that could be used as a single. Which is why "Wild Honey" was cut in late September, with Brian apparently thinking that he could then bounce back and forth from various projects. As it turned out, "Darlin'" was a bigger hit than "Wild Honey," and drove the WILD HONEY LP sales in the first months of '68.
But that's the "forward-facing" territoriality, if you will. What about the "backward-facing" territoriality? If the "10-track SMiLE" and Brother Records were both kiboshed in fall '67, did Brian throw up his hands about the SMiLE material right then and there? The amount of "Child" in "Little Bird" isn't enough to kill off a return to SMiLE, but a family ultimatum that Brian had to see through a transition to a fully functioning band (meaning songwriting/production as well as their already-separate touring) before venturing out to work with outside artists could have done so. Something changed regarding this in the fall-winter of '67-'68. And then something changed in Brian after those sessions he led after FRIENDS that stalled out with only two released songs ("Do It Again" and "I Went to Sleep"), which led to a scramble in the fall to come up with tracks. This was Brian's first real "fallow period," with no new songs (though folks suggest he was still involved in some of the sessions, such as the first "Cottonfields").
It's clear that the downward spiral for Brian, where the "manic" phase mostly disappears, occurs in the second half of '68. What did the escalating tug of war over the remaining unused SMiLE tracks have to do with that? And how much of it was his desire/need to withdraw from a situation where he'd tried to have some cake and eat it too on FRIENDS, and becoming vulnerable to backlash when the LP tanked?
I'm not trying to "go Gaines" on this, but there are still some unanswered questions here that can illuminate some of the remaining dark corners in the time frame, corners that certainly appear to stem from the lingering effects of SMiLE.