Is there a difference between the command line tools that come with xcode and the ones installed with
xcode-select? If I install xcode and then run
xcode-select --install will the ones installed with xcode be overwritten?
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.
If I recall correctly it downloads the xcode tools command line package, which is part of the main xcode distribution. I wouldn't expect it to download anything at all if the command line tools are already installed.