Gtk configurator has been replacing .gtkrc-2.0 config file with it's own settings, discarding present file contents. Now it only modifies configuration strings, or add them if they are not present at the beginning of the file.
This patch also removes redundant configurations, such as including theme from /usr/share/themes gtkrc's, "user-font" style, widget_class and unneeded symlink .gtkrc-2.0-kde4. Those options do not seem needed, as gtk2 applications look the same without these options without any regressions. This was tested on Gimp, Inkscape and BleachBit apps on Manjaro, OpenSUSE and KDE Neon distributions.
As for gtk3 ini file - this is not reproducible anymore, any line, which does not hold parameter changeable in configurator, remains in settings.ini.