QGuiApplication::setPalette and QApplication::setPalette are two distinct static functions and when the paletteChanged signal was introduced in QGuiApplication the latter was never adjusted.
SystemPalette connects to this signal to avoid installing an eventFilter on qApp for ApplicationPaletteChanged.
This causes e.g. QML-based System Settings modules to not update when changing color schemes but only the widget-based application around it.

Switching to Breeze Dark look and feel theme now updates the background of the QML parts. There's still some glitches like QQC buttons not repainting properly but at least it's not as embarrassing to look at as it used to be.

I'm trying to fix this in Qt but until this is in I think this patch is safe either way and will also benefit users of older Qt versions.

https://codereview.qt-project.org/#/c/181704/