As you can see below, my Xft settings match exactly my fontconfig settings:
$ xrdb -query | grep -i xft
Xft.antialias: 1
Xft.autohint: 1
Xft.dpi: 96
Xft.hinting: 1
Xft.hintstyle: hintmedium
Xft.lcdfilter: lcddefault
Xft.rgba: none
$ fc-match --verbose :family=Mono:size=12 | grep '^.\(hint\|anti\|auto\|dpi\|rgba\|lcd\)'
antialias: True(w)
hintstyle: 2(i)(w)
hinting: True(w)
autohint: True(w)
dpi: 96(f)(w)
rgba: 5(i)(w)
lcdfilter: 1(i)(w)
Unfortunately Xft seems to be ignoring these settings, and is doing no hinting at all. I can see this in GUI Emacs or running the command
pango-view --backend=xft --font='Mono, 12' -t 'Xft - X FreeType interface library'
Compare the rendering with the one produced by the Cairo backend:
pango-view --backend=cairo --font='Mono, 12' -t 'Xft - X FreeType interface library'