The paid addon is definitely better, but if you want to do the hard way, based on your example you'll need to:
- Put the objects you want to isolate in a collections, eg. Cube in Collection A, Sphere in Collection B, then Cone in Collection C, and everything else in Collection D (light, camera, etc)
- Setup 4 View Layers: eg. named "All", "Cube", "Sphere", "CubeSphere".
- Then for rendering all, you use viewlayer "All", and leave everything in place. for viewlayer "Cube", uncheck all collections from Outliner except collection A & D (Cube, light, and cameras), for Cube and Sphere together, you only check the collections with both, do the same with others.
- In Output properties, check **Stereoscopy**, then select Multiview.
- Uncheck the default RenderViews "left" and "right", then add 2 new ones and rename them (if you want), then for each, use different suffix at Camera Suffix. Rename your cameras accordingly. eg: Camera_1 and Camera_2, the suffix should be _1 and _2.
- Render, then after render is done, in the *top right* of render result, you can see drop down of each RenderViews, according to what you rename them from step 5 above. From Layers drop down, you can see result from each ViewLayer from step 2. Save each image with Alt + S, OR you can setup File Output node from each ViewLayer (Render Layers node) in Compositor if you want to automate file output.
LIMITATION (possibly bug): ViewLayer/ Render Layers node in Compositor doesn't have option for multiple cameras, means each will actually output 2 images (if you have 2 cameras). So if you setup File Output node from each Render Layer, they will produce 2 files, that leads to another bug: you won't see backdrop from Viewer node because consisting of 2 images.
another bug I found: if you setup multiple File Output nodes with same output folder, it will overwrite the renders of other Render Layers, then the result files will have black background even if you use Transparent option for background/world, while the actual render results in image editor are fine.