For those wikipedias that /should/ be using the same codebase, it seems reasonable to me that they should have all of the scripts symlinked to the scripts of the main wikipedia. Then, any configurable variables could be exported by Apache as ENV variables. By doing this, you avoid running a script to update things, a person doesn't have to update them manually, and all of the apropriate wikipedias will be running the same software...

That will work wonderfully up to the first time we make a software update that requires a database change. In that case, we want to make sure that the upgrade process incudes the database update, and each one has to be done individually.