Even though the check metadata consistency machinery is supposed to read at snapshot, when using the DBDirectClient we don't take into account the command's readconcern. This means we end up executing the command with read concern local and that can cause checkMetadataConsistency to read inconsistent data.

This exact same problem was solved in SERVER-79357 by making RSLocalClient::runAggregation set the readConcern in the Operation context directly, however SERVER-99966 changed the logic and started using DBDirectClient directly.