Cannot configure a Mongo replicaSet from docker init script

Question

I am trying to set up a 2 node replicaSet in docker for local development only. Single node already works fine, but there are keyfile issues when trying to add a member as part of the docker init script (NB I see the keyfile is set correctly from the logs). The same command works fine from a shell though, not via the init script.

Basically, the current config has worked fine for one node, but adding another gives the following error:

mongo_1            | {"t":{"$date":"2021-07-21T16:33:19.583+00:00"},"s":"W",  "c":"REPL",     "id":23724,   "ctx":"ReplCoord-0","msg":"Got error response on heartbeat request","attr":{"hbStatus":{"code":13,"codeName":"Unauthorized","errmsg":"command replSetHeartbeat requires authentication"},"requestTarget":"mongo-secondary:27017","hbResp":{"ok":1.0}}}
mongo_1            | {"t":{"$date":"2021-07-21T16:33:19.583+00:00"},"s":"E",  "c":"REPL",     "id":21426,   "ctx":"conn2","msg":"replSetInitiate failed","attr":{"error":{"code":74,"codeName":"NodeNotFound","errmsg":"replSetInitiate quorum check failed because not all proposed set members responded affirmatively: mongo-secondary:27017 failed with command replSetHeartbeat requires authentication"}}}

If I remove mongo-secondary from the set, then after startup use a shell to mongo to load the exact same config, everything works fine (they keyfile is used and the set is made with both members).

Currently my config is:

# docker-compose.yml

  mongo: &MONGO
    image: mongo:4.4
    restart: unless-stopped
    volumes:
      - mongo_data:/data/db
      - ./scripts/docker/mongo/001_mongo_init.js:/docker-entrypoint-initdb.d/001_mongo_init.js:ro
      - ./scripts/docker/mongo/mongo-entrypoint.sh:/mongo-entrypoint
      - ./conf/mongodb/mongod-config.yml:/etc/mongod.yml
    entrypoint: sh /mongo-entrypoint
    ports:
      - 27017:27017
    env_file:
      - ./env/mongo.env
    command: --auth --config /etc/mongod.yml
    extra_hosts:
      - mongo:127.0.0.1

  mongo-secondary:
    <<: *MONGO
    volumes:
      - mongo_secondary_data:/data/db
      - ./scripts/docker/mongo/mongo-entrypoint.sh:/mongo-entrypoint
      - ./conf/mongodb/mongod-config.yml:/etc/mongod.yml
    ports:
      - 27018:27017
    extra_hosts:
      - mongo-secondary:127.0.0.1

# mongo-entrypoint.sh

#!/bin/sh

set -eu

# Create the keyfile used for mongo replicaSet auth.
keyfile=/home/keyfile
echo "Creating replicaSet keyfile..."
echo "keyfile" > ${keyfile}
chmod 0400 $keyfile
chown mongodb $keyfile
echo "Created replicaSet keyfile."

# original entrypoint
exec docker-entrypoint.sh "$@"

// 001_mongo_init.js

function getEnv(envVar) {
    const ret = run('sh', '-c', `printenv ${envVar} > /tmp/${envVar}.txt`);
    if (ret !== 0) throw Error(`Value "${envVar}" is not present in the environment.`);
    return cat(`/tmp/${envVar}.txt`).trim(); // NB cat leaves a \n at the end of text
}

// create replicaset
const rsconf = {
    _id: getEnv('MONGODB_REPLICA_SET'),
    members: [
        {
            _id: 0,
            host: 'mongo:27017',
        },
        {
            _id: 1,
            host: 'mongo-secondary:27017',
            priority: 0, // prevent from becoming master
        },
    ],
};
rs.initiate(rsconf);
rs.conf();
// further code to create users etc.

# mongod-config.yml

---
security:
  keyFile: /home/keyfile

replication:
  replSetName: rs0
  enableMajorityReadConcern: true

Cannot configure a Mongo replicaSet from docker init script

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