All file formats have a format. If you know what that format is then you can test for it and, if you find it, you can then assume that the file is that format. You need to know the format for every file type you want to be able to identify.

I could be wrong but from what you've said I'd guess that this ApplicationXtender probably stores a file's type in its database before changing the extension. It then uses that information to identify the format instead of the actual extension.