Can confirm that simply using application/vnd.docker.distribution.manifest.v2+json instead of application/vnd.oci.image.manifest.v1+json when pushing images to registry.fly.io fixes the 404 issue and I can start Fly machines with the images I’m pushing, including layers that are tar+zstd encoded 
Still have to confirm that they are functioning properly (a bit of image config to do) and will report back when/if I get that sorted.