Using layer visibility in Movie Render Queue - rendering an image in layers without stencilling

I need to render some high quality stills in layers to be assembled and edited in Photoshop. Previously I would use layers to hide and show groups of objects and do a high res screenshot. Movie Render Queue provides a much more robust and higher quality render but I can’t find a way to easily render layers like this. Of course I can use the stencil clip layers function in the deferred render tab but then the background will have holes where foregrounds elements (characters) are. It would be ideal if at minimum MRQ would respect layer visibility and better still allow you to key layer visibility. Better than all of that would be for MVQ to be able to render layers without stencilling them out but I can see that might be harder. MRQ could render layers in this manner in multiple passes though even though of course it would be much slower. I am being asked to render dozens of single frames and each frame needs to be rendered in maybe 5 layers and some layers may have 100s if objects in and those objects may live in multiple levels. It’s very laborious currently. I would imagine for the blossoming VFX industry usage of Unreal, this kind of feature would be incredibly important too.