It's a little more complicated than that, actually. Any given application of a file format may use various obfuscation techniques on the file's header or contents that render the file invalid from the perspective of the published standard (if there is one; it is also common in these cases to change the file extension to further disguise what format the file actually uses). Programs that do this may or may not de-obfuscate the file prior to use, depending largely on how and why the file was obfuscated.

For instance, a common obfuscation method is simply removing the magic number from the file; in this case, the program may simply try to use the file as the given format and return an error (or crash; we are talking largely about proprietary software in these cases after all) if the file can't be read.