Yes, if multiple apps use the same bundle identifier, they will be recognized as the same app - but you can't have multiple apps with the same identifier in the App Store or on the device!
There is currently no way to share files between different Apps (with unique bundle identifiers) via the local file system. You can pass some data with custom URL schemes from one running app to another, but I think that's not what you're looking for.
Apple's suggested way of dealing with this situation is to have just one app, and implement In-App purchases to upgrade to the full version.
Here's a very similar SO question: Share data between two or more iPhone applications