The 'blob:url' retreived with FileChooser.FileURLAt(Index) is only valid during 'this session'.
The next session the same file will have a different 'blob:url'.
In other words : it is a temporal value, only valid during 'this' session.
Hence, even if you store it in the Local Storage, it has no meaning the next session.
I dont think that Scirra will ever release something/anything that could be a security treat in any means.
I suppose there are plugins (In Cordova package, Phonegap package, packages like those, dont know how many there are) to list user files on mobile. But i never used those. Sorry.