The problem with the official Apple fix is that it does not include all the files and folders that are included in the update. At least for some users, there are also files to be installed in Application Support and in the System Library (as opposed to the regular Library). The greatest problem I noticed was with the Compressor folder in Application Support, which the Apple Installer actually trashed instead of updating with its included files. Installing with Pacifist took care of all this.
In regard to permissions: Yes, after installing with Pacifist, there were a number of permissions that had to be fixed with Disk Utility. But that was also true after first trying to install with the Apple Installer. In other words, the incorrect permissions are in Apple's update, and are no fault of Pacifist. Also, there were NO ACLs on my system after installing with Pacifist, so the user who found those had probably gotten them somewhere else.
As for the dates on the files: Look at version numbers, not creation dates. If there's an older date, then it's probably because Pacifist is only updating the files that need it.
Several days after installing with Pacifist, I'm experiencing zero problems. For all of you spending loads of time with Apple Support with no resolution, you might try the easy way!
Aaron Shepard