What I don't like about programs which use those standards is that when I reinstall Windows, I often forget to backup those directories and so, most of the time, I lose the config of some programs (even with a backup function in the programs, I don't always think about backup everything), or worst, some savegames of some PC Games.
With programs which store the configuration in their own directory, as I install most of them in a separate hard drive, even if I forgot to backup them, I can still rename the old directory, reinstall them if required, then overwrite the folder with the old one to get back the configuration settings.