It looks like the ApplicationWindow is not affected by the QGuiApplication's palette values.
My environment is Qt 5.12.5 on Linux. I started over with an empty project to make sure of my results.

main.cpp:

    QCoreApplication::setAttribute(Qt::AA_EnableHighDpiScaling);

    QGuiApplication app(argc, argv);

    QPalette palette = QGuiApplication::palette();
    QPalette newPalette(palette);
    newPalette.setColor(QPalette::ColorRole::WindowText, QColor("#00FF00"));
    QGuiApplication::setPalette(newPalette);

main.qml:

ApplicationWindow {
    visible: true
    width: 640
    height: 480

    Component.onCompleted: {
        console.log("Text color : " + palette.windowText)
    }

    Text {
        text : "hello"
    }
}

Logs "Text color : #26282a"
What am I missing if we refer to the documentation?