True Type fonts, for example, in the /usr/X11R6/lib/X11/fonts/TTF/ directory are not used by XFT, as that directory is not listed in fonts.conf. fonts.conf should, by default, contain the same directories as listed in /etc/X11/fs/config when said directories fonts are supported by both systems.
The font in /usr/X11R6/lib/X11/fonts/TTF/ are deliberately excluded because they duplicate the fonts in /usr/X11R6/lib/X11/fonts/Type1, but are rendered worse. If you are installing custom fonts, they should go in /usr/share/fonts.