I see…
Indeed if I move Master section to my primary display then plugin windows can be shown at the same time on secondary display on top of the Control window just as expected however this is not ideal for me.
BUT I perhaps found a workaround by undocking the Master section (made it floating) and disabling fullscreen mode of Control window on my secondary display and resizing it manually right next to the Master section = visually all looks almost like before (e.g. Master section embedded into Control window) but plugin windows are shown at the same time as expected…