From what I understand, is that you submit the app (basically, the uncompiled source code + assets + key) to the google store. The store keeps the app in that format. Then, when the device need a copy of the app, that info is sent over the network to the device. Then the device compiles the files and you have your app. Network communications is easily intercepted. Therefore, you can get the "App" in the source code + assets + key format, before it even touches the compiler.
Anyhow, we'll all see more with the SDK coming out in less than 9.5 hours.