xcrun just locates tools inside the current $DEVELOPER_DIR, which is inside the Xcode.app bundle (based on which Xcode is selected with xcode-select). You can think of xcode-select as virtualenv or similar systems: you select which version of the tools you want to use.
Fun fact: If you symlink xcrun as a different name, it will assume that is the name of the tool you wish to run. So "ln -s /usr/bin/xcrun altool" will make altool an alias to run the version of altool bundled with the currently selected Xcode.
Fun fact: If you symlink xcrun as a different name, it will assume that is the name of the tool you wish to run. So "ln -s /usr/bin/xcrun altool" will make altool an alias to run the version of altool bundled with the currently selected Xcode.