Command Line Tools Difference?
Xcode has command line tools embedded in its application bundle that are used by the Xcode IDE as needed and are separate and apart from the Command Line Tools for Xcode package, that can be downloaded by itself, which installs outside of the application bundle. The separate package can be installed and use without having the Xcode application installed.  As to versioning, I believe as each version of Xcode is available a corresponding version of the Command Line Tools for Xcode package is also made available and for what's included in common should be the same versions.  When installing the Command Line Tools for Xcode package with Xcode installed it does not overwrite the Xcode.app bundled command line tools, they are updated as Xcode is.