getQueryLog only reads logs from Background thread scope. If parallel execution is set to true, a new thread is created for execution and all the logs added by the new thread are not added to the parent Background thread scope. In replication scope, replStateLogTasks are started in parallel mode causing the logs to be skipped from getQueryLog scope.
There is one more issue, with the conf is not passed while creating replStateLogTask during bootstrap load end. The same issue is there with event load during incremental load. The incremental load end log task is created with the proper config.