Currently you can set options for Qt apps and GTK apps separately, but it would make much more sense to set the options for GTK apps in the respective KCMs too, instead of separately in the GTK KCM.
Here are the Bugzilla tickets tracking the individual work items for this:
[ ] Fonts: D21860 (fixes https://bugs.kde.org/show_bug.cgi?id=138866)
[ ] Icons: D24543
[ ] Cursor theme (fixes https://bugs.kde.org/show_bug.cgi?id=401507)
[x] App color theme: D22877 (fixes https://bugs.kde.org/show_bug.cgi?id=400101, https://bugs.kde.org/show_bug.cgi?id=356006, and https://bugs.kde.org/show_bug.cgi?id=357524)
[ ] Scrollbar click settings