I tested with gtk2 2.24, gtk3 3.22 and freetype 2.8 on current Debian testing (it may or may not work with older versions): If there are no xft-related settings in gtk config or xrdb, all gtk apps are correctly conforming to fontconfiig configuration. There were some issues a year ago, now there seem to be none left.
So it would be great if lxappearance dropped font settings from gtk config files and wrote them to $XDG_CONFIG_HOME/fontconfig/fonts.conf