What happens if you create another folder alongside the Contents folder in an application bundle?
It wouldn't be that bad except for the whole completely using app packaging completely incorrectly. Anything inside that app won't get indexed by spotlight, if you delete that app then all notes and references are also gone. 

I can't think of a sensible use case where this would be a good idea. Unless of course you are an app developer and you are wanting to store things during app execution. 

I would not recommend doing this even though it should technically work.