In section 8.2.1 in step 2 we are not providing the location of the CPE files that are part of the image. Without it, Clair cannot know where to look for them. CPE files in the Clair image are located under the /data directory so the complete config that should be applied to the clair-config.yaml file in the init config bundle should be:

indexer:
  airgap: true
  scanner:
    repo:
      rhel-repository-scanner:
        repo2cpe_mapping_file: /data/repository-to-cpe.json
    package:
      rhel_containerscanner:
        name2repos_mapping_file: /data/container-name-repos-map.json
matcher:
  disable_updaters: true

Thanks!