Okay - after having done some more digging, it looks like the PureMVC MooTools js port is the way to go for JS based AIR apps.
I haven't done anything with MooTools to date, but must say that it looks like the perfect match for PureMVC! Not having a good way to organise my js code properly in a larg-ish AIR app has been the one thing holding me back from giving the tech a proper try.
Sorry for the noise with the above questions! If I get it all working and manage to grok PureMVC, would be happy to share any insights I might garner...