The article also explains why an update package may have more then one copy of a given file. Each update will have a copy of the relevant file for each "cardinal point" in the file's lifecycle. The cardinal point, a new term to me, are the main releases of the file (ie RTM and for each Service Pack). So copies of a file will exist for RTM, SP1, SP2 (when it exists) as well as for a given hotfix.
An interesting read!