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/