Similar questions on here seem to refer to rendering two different scenes for the purpose of multiple outputs. I want to composite BOTH scenes together in Blender's compositor and then export as one file. It is an animated image sequence. When I hit F12 in one scene, with both scene files setup and joined by an Alpha Over node, only the first scene renders. The second scene has a single render layers node joined to an output node. Not sure what's wrong with my setup? Is this a possible bug? I'm using Blender 2.81.3. Thanks.
I thank God for showing me the solution: all you have to do is create a new, blank 3rd Scene (with no objects or cameras) and composite the other 2 scenes there in the compositor. Now when you hit render from the 3rd scene, both scenes will render and one file will be output. Be sure to set your color management settings AND the desired frame output range in the 3rd scene, as it will OVERRIDE whatever settings you have in the other scenes.
For example, this allows you to do special compositing hacks with EEVEE, which currently doesn't support the "holdout" or "indirect only" passes for Collections. However, you can use a "holdout" material on individual objects and create masked areas from that. This is how you can workaround flickering ambient occlusion in EEVEE that is caused by thin objects. In one scene you have AO turned ON, and in the other scene you only render certain objects with AO OFF; then composite them together in the 3rd scene.
Each of the other individual scenes you want to composite should have at least an output node connected to its renderlayer, like this: