I added 8 or so Ext @require's to the externalized shim, and achieved a functioning build!
We have added a compiler metadata command to export these symbols and informed Bryntum of this feature. They can (if they chose) provide the symbols file needed to use the obfuscated flavor of their (awesome ) library with Sencha Cmd.
Thanks for all your help getting to the bottom of this.
Director of Engineering - Frameworks (Ext JS / Sencha Touch)