The combo updaters from Apples website, I guess, is most often used for offline installs. They can be downloaded, and installed at any time one wants.
Some people might not use the app store at all, and would prefer to download a file, like with a lot of other applications.
I do usually keep a combo updater on my USB drive, just in case a friend needs an update to their Mac, and have no, or a slow internet connection.