I think the title says it all, but the problem is bigger than that. The whole idea that the last 3 or 4 letters of a filename are an indication of underlying file format and structure is flawed. More than flawed, it’s wrong, but 3 decades of MS-DOS (yes, it’s still part of Windows) and its usability nightmare known as filename extensions is hard to overcome.
Interestingly, I don’t blame Microsoft for this particular confusion though, since it was Apple that broke the generally accepted, or de facto, standard in this case.
With the release of OS X, Apple introduced a new kind of file — or really a folder that acted and looked like a file to the user — called a package. The idea was that the insides of certain folders were only for system usage and should be hidden from users. For example, applications and all the various libraries and resource files and executables were packaged into a .app folder. To the end user, this .app folder looked and acted like a standard file and it could be double-clicked to launch the application. Early versions of Mac OS X even hid this package extension from the user, but to this day, to see the contents of a package, you have to “right-click” or “control-click” on the package and select “show package contents” to see what’s inside.