The files in conf.avail/ (symlinked in conf.d/) are there for system wide configuration. The use of "append" there is right, because that leaves the choice to each user to change their config, if they want (using "assign" in ~/.config/fontconfig/fonts.conf ). The problem arises because fonts options in the desktop environment usually override the default fontconfig configuration, even if you don't touch any fonts setting in the DE. For example Gnome3 default config enable the autohinter and set the hintstyle to "full". If you enable subpixel hinting in conf.d/ you will get a fuzzy result, because autohinter is not designed to work with subpixel (the subpixel setting is not override because Gnome3 defaults doesn't touch this option). The best thing to do is to set the DE fonts settings to be equal to the conf.d/ settings and/or the user's settings (in Gnome3 you can change settings with gnome-tweak-tool), because DE fonts settings will have always the highest priority, at least on Xfce where I'm testing it. BTW it looks like Gnome and Xfce (and maybe others) uses Xft, that have priority on fontconfig: maybe the bug should be reported to the DEs teams to make them use fontconfig instead of Xft?
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