I hardly like to say this, but, with the greatest respect to both you and Hall & MacGregor, these are merely the standard verses printed in hundreds of popular song anthologies and selections from Burns, and learned by most of us at school; though with a few very minor differs of no significance due either to Hall & MacGregor or to your ear. They add nothing to a discussion of the history of the song.

If you have any new information to add on the question of the tune as explored above, that would of course be welcome.

Let's return to the matter in hand. In answer to Q, the notation in the 1853 edition of SMM is the same as in the original edition: if Burns' anecdote is accurate, Miller's melody as polished up by Clarke. That doesn't explain the obvious differences between the SMM notation and those printed by Gow and Dale or the MS example, though. There is clearly more to the story than we know so far.