Found the answer to this as the last post in the thread:
I added the following to the sencha.cfg within the .sencha\workspace folder.
workspace.build.dir=C:/builds/TolMobile
Not sure why packager.json contains an output path with the following:
"outputPath":"../build/",
It doesn't seem to even be used. If its redundant why don't they just remove it? In addition I still haven't got their command line arguments to work either. Strange.