Since the XQuartz X11 package clobbers Apple's X11.app, their software update will clobber the XQuartz X11 package. OS X Software Updates have included some of the work done by the XQuartz project, but for various reasons, Apple cannot ship the latest and greatest version offered by the XQuartz site. Together with supporting libraries and applications, it forms the X11.app that Apple shipped with OS X versions 10.5 through 10.7.
The XQuartz project is an open-source effort to develop a version of the X.Org X Window System that runs on macOS.
