This is silly. Imagine the nightmare if every single application was using a password to protect its files.
The operating system is in charge of the file system security. Not the application.
All files are equal. Some are more equal than others.
No, because even the ability to create files in your directory is way to the theft of these "more important" files
Therefore it make sense to take care of some file more than others. Whether that is done through the application itself or the operating system is irrelevant.