http://bugs.winehq.org/show_bug.cgi?id=23097
--- Comment #18 from Alexandre Julliard julliard@winehq.org 2010-06-23 03:32:45 --- Xft resources take precedence because in general you want the config to be specific to a display. If you log into a remote box and display an app on your desktop you want the app to use the same settings as the rest of the desktop, not the fontconfig settings of the remote box.
Note that fontconfig doesn't always take precedence for native apps either, it's more complicated than that, and it differs between apps and desktop environments. It's a big mess, there isn't one correct solution that Wine could simply follow.