Well this depends on the package...
Let me describe an example
i repackaged the quicktime 7.4 Setup from native Exe to MSI and cause any update information (Auto Update enable/disable etc) is stored in the registry i created on the Admin Studio (after successfull install monitoring the setup) Workstation a exported reg File (with the hive, which contains the Update Settings for Quicktime) and after that i coud include this File within the setup process) For this the inclusion Function is very handy...
But for standard setups it fits the best, if you don't modify any settings there, cause in extreme cases you can kill the whole client