One question though; where is a sensible place to set any extra arguments that are passed to mxmlc at compilation time (Apple-B)?  I need to add a -default-size argument to the compiler but can't see where.  I don't want to edit the build script but I want to put it in the 'right' place.  Is there a project specific variable I could use?

There are two ways to do this...

By default mxmlc will also search for a config file in the same directory as your Main.as or Main.mxml file with a -config.xml suffix (so Main-config.xml).