'...the grid-fill seemed impossible without an additional piece of information from the extra letters (ie, the message has to make sense, resolving one last ambiguity).
I mean, that's tight setting. Squeezing everything out of the puzzle.'
I didn't misunderstand your praise for the setter, but you appear to suggest it's the grid-fill that requires the additional information.
For the 'message to make sense' some letters having questionable codes can be repositioned using alphabetical order a second time. The fact that a final ambiguity is resolved doesn't effect the grid-fill as a whole. For that process to work you'll need the extra letters from the cold-solved clues.
You also appear to have solved most of the clues before starting on the fill - but with hindsight you 'think', 'perhaps' this wasn't necessary, but how can you know this after the fact?
I don't wish to argue over the details - if you believe this is a puzzle without any flaws we can disagree and leave it at that.