I'm not saying this is a huge problem for me even if it bothers me personally. But if you're here on HN advocating native over Electron, then it seems logical to me that you would care about being truly native instead of merely "using native controls while feeling off".
This is even before getting to the point that Qt isn't truly native. They just draw controls in a style that looks native, they don't actually use native controls. wxWidgets uses native controls but they don't behave better despite that.