Plenty of smaller sections were completed, like Our Prayer, but there was no indication which of those were intended to be small stand-alone pieces, which were intended to be a part of a larger song, and which were ideas that Brian would have fleshed out and developed more but never got around to doing so. we just treat those pieces as if they were always intended to be that way because that's all there is.
the official release of Smile was assembled so well that it makes it sound a lot more finished than it actually was at the time. Even Brian didn't know how it would all go together. I don't think he figured out how the pieces would all go together until he'd put together his solo version of Smile (the 3-part structure to the album at the very least wasn't figured out until then). And then that gave them a model to shape the Smile Sessions version after.
Big parts of Smile that sound like they're complete songs on the officially released versions were never actually finished at the time. "Surf's Up" for instance. Brian had only recorded a backing track for the first portion, but no overdubs and almost no vocals. Cabinessence was basically done at the time, but Carl's vocals weren't recorded until the 20/20 sessions. Even the single version of "Heroes And Villains" didn't fully come together until Smile was already officially scrapped and those early versions just sound like a bunch of random sections with no cohesive order. some of the bits which are in the official version were recorded in that weird post-Smile/pre-Smiley period.
There would have been no indication as to what pieces belonged in full songs and which were songs unto themselves. "In The Cantina" and "I'm In Great Shape" are both 30 second pieces of music. but one is in the 1st category and the other is in the 2nd. But both were originally part of Heroes and Villains. If Brian wasn't willing to make those decisions at the time none of the other band members would have had a clue what to do with the pile of scraps that were lying around.
During previous Beach Boys albums Brian would usually work on one song until it was finished and move on, but on Smile he would work on something and abandon it moving on to the next thing (or returning to mess around with Heroes and Villains some more). Nowadays we can lay out the whole thing on a computer and piece it together, but without that technology nobody could have seen the bigger picture at the time.
Nonetheless I'm generally of the opinion that with the exception of the obviously unfinished songs ("Do You Like Worms", "Holidays", "Love To Say Dada", and "Look") the Smile Sessions version is probably better than what would have been released at the time if the band had actually completed it in 1967.