storage.api.server: Align configuration structure

This should fix the swh-docker-dev ci failure [1]

Related to D4272

• [1] https://jenkins.softwareheritage.org/job/swh-docker-dev/lastBuild/console

Test Plan

tox

doco up swh-idx-storage starts without failure [1]

• [1]

$ grep swh-idx-storage -A3 $SWH_ENVIRONMENT_HOME/docker/docker-compose.override.yml
  swh-idx-storage:
    volumes:
      - "$SWH_ENVIRONMENT_HOME/swh-indexer:/src/swh-indexer"
$ doco up swh-idx-storage
...
swh-idx-storage_1               | [2020-10-16 08:30:27 +0000] [1] [INFO] Starting gunicorn 20.0.4
swh-idx-storage_1               | [2020-10-16 08:30:27 +0000] [1] [DEBUG] Arbiter booted
swh-idx-storage_1               | [2020-10-16 08:30:27 +0000] [1] [INFO] Listening at: http://0.0.0.0:5007 (1)
...

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Migrated from D4280 (view on Phabricator)