In order for everything to work as it will be indicated in the config - you need to make these settings before the mongodb server is first started

storage:
  journal:
    enabled: true
  engine: wiredTiger
  directoryPerDB: true
  wiredTiger:
    engineConfig:
      directoryForIndexes: true
      journalCompressor: zstd
    collectionConfig:
      blockCompressor: zstd