When creating a Runtime application, the runtime options can be set to also remove the Admin account for Full Access. That keeps the file from being opened with Full Access, which affords some slight additional protection, though it also means that you have to return to your original pre-binding copy of the FMP file to make any modifications, and then rebind it again after making changes if you ever want to update it.
If you decide to go that route, be sure to save the binding Settings to reuse each time you rebind so the new modified file will be compatible with the previously-generated Runtime app.
Using the runtime option will not make it harder to reverse engineer your file. The remove full access option that Stephens mentioned is a good idea but you can use this without the runtime option.
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What rgordon says is quite true; it's simply one option of the Developer Tools, which includes creating runtimes. In fact, removing Full Access to a file without turning it into a runtime would probably be better, as it avoids confusion over the file extensions that runtimes use in place of the standard FileMaker extension.
Removing Full Access without making a runtime will still require you to go back to an unaltered copy of the file (which allows Full Access) if you want to make future modifications to the file yourself, and then remove Full Access with the Developer Tools on the distributed copy again each time after you make file modifications.
Keep in mind that, while someone may be able to use cracker software to force an unrestricted file open in Full Access, the security you set in the file for standard users is the first obstacle you need to place and refine for keeping users from messing with the file or exposing its structures.
I'm concluding that, from a security standpoint, there seems to be no advantage to a FM13A run time over a standard FM13A db for use on the iPad or iPhone.
EAR is not officially supported in Runtime. If you are crazy about security that may be something else you want to look at.