After using OS X for years, I've seen so many cases for pixi hacks on the systems. And every time Apple pushes out a software update, so many griefs are created on both sides... Both the users of the hacks and the devs who are assigned to investigate on root cause. Root cause analysis is time consuming and seriously frustrates the devs if they are hunting for ghosts due to an unintended system modification.
That's why if the update file is going to modify the configuration directory, I want to appeal to the author of the file to include a change on the version string. Such that those bug report will indicate a change on the system file.