I appreciate your response!
You are probably right and after a bit of distance from this one I think I'll bump it up to an average mission (I also noticed that my ratings by category should be an overall 5 not a 4, so the bump up is definitely appropriate).
In essence this is a very creative set of missions I just found the execution subpar and would have rated it higher if it had been more enjoyable to play. The annoyances I mentioned above lead to me getting more frustrated by the minute...
I'd pursue your idea with the changes appearing in the notes. There are sometimes multiple entries for T1 or T2 FMs as well but these are often different releases and not updates (e.g. the Scarlet Cascabel).
Having a kind of changelog in the notes sounds perfect to me and circumvents any confusion