Thanks to u/jesus_is_imba on Reddit for the following answer:
ffmpeg -r 24 -i my_images_%04d.png -c:v libx264 -crf 18 -preset slow -g 48 -pix_fmt yuv420p -movflags +faststart output.mp4
The -g argument defines keyframe interval in frames and according to Oculus should be 2 seconds, ie. 2x your frame rate.
This command produces video that plays back ...
Format: h.264 -> that's what makes it look bad.
h.264 is a codec in the mp4 container and always compresses, making the file smaller and look worse. For lossless exporting you use prores 4444 xq if you're using mac (or windows with the newest version of premiere) or DNxHR. I highly recommend prores 4444 xq though.
The answer to your question is yes. Masks, solids or multi-compositions will help.
What, you want more? Oh ok.
Thing about After Effects is that there is almost always at least two valid ways of doing anything:
To fix your problem you could use masks on each eye. Now because you're scaling the layers, and masks are attached to a layer and scale with it, ...