All features are identical.
However, which version you need to use depends entirely on what kind of Windows you're using. Windows 3.1 is a 16-bit operating system. You must only use the 16-bit version of the Netscape Navigator on Windows 3.1. Sometimes, when you try to install the 16-bit version of the Netscape Navigator on Windows 3.1, it will complain that an outdated version of Win32s is present. This is because a Win32s installation replaces some of the 16-bit .DLL files which the Navigator requires, and the Navigator can tell that the .DLL files which Win32s put there are too old.