I think the author's primary point is, "Merging changes sucks, don't make your users do that," with a corollary: if your program loads configuration from a directory that is only populated by the user, there's nothing to merge and thus never any merge conflicts. Case in point: /etc/polkit-1/rules.d. I can add whatever rules files I want in there and they're never going to conflict when I update. If PolKit makes breaking changes to the format, it will log errors somewhere and I can look at those errors, look at my rules, and figure out how to fix them. That's a hell of a lot easier than merging conflicting changes to code/configuration.