Due to the fact Scene3DRenderer only adds a Depth attachment to the final FBO (scene3drenderer.cpp:183):

QOpenGLFramebufferObject *Scene3DRenderer::createFramebufferObject(const QSize &size)
{    
QOpenGLFramebufferObjectFormat format;            
format.setAttachment(QOpenGLFramebufferObject::Depth);    
return new QOpenGLFramebufferObject(size, format);
}

While it does not cause any issue when using multisampling since that FBO is only blit'ed on (it could just not use any attachment for that matter), Scene3D will directly use that FBO for drawing when it is off, leading to a lack of stencil support. It could instead add the CombinedDepthStencil to the final FBO when multisampling is off, none otherwise.