Looks like we can't reproduce the issue or there's a problem in the test case provided.
app.js designer.js and Application out of sync
I don't think that I can reproduce this but it is a nasty problem when you run into it. My best guess is that I did not save the project before I walked away from my machine last night and windows update forced a reboot.
Today I added two models and stores but when I did Ext.data.StoreManager.lookup(NewStore) the store was not found. Looking in the Application (code view in the Architect) the stores and models were defined but when I looked in the debugger they were not in the array of stores in Ext.data.StoreManger and I could not find them in the files to debug in Chrome.
After lots of investigation, I found that they were defined in the app.js file but they were not defined in the designer.js file and some old files were defined there that had been renamed (this sounds backwards but I am pretty sure that it is true).
Again I don't think that I could give you a solid reproducible case but if there is a way to check for consistency between these it would have saved me the better part of an afternoon cleaning it up.
designer.js is a legacy file that you can delete if you would like.
It looks like the base directory under stores is legacy as well. So I assume that the problem was inconsistency between Application and app.js
Yes, this stems from the change from subclassing to using overrides.