Oracle 11gR2 – RMAN Archivelog Backup Guide

If my source database uses SPFILE then do I have create a PFILE from the SPFILE?

Yes, you need to create a temporary PFILE to use while duplicating the database. You will later switch the new instance to use the SPFILE.

Use

CREATE PFILE = 'path/to/pfile' FROM SPFILE;

You only need to create directories that are referenced in the PFILE or SPFILE. Which directories need to be created?

You will start the database as NOMOUNT to begin the duplication. This means the controlfiles will not be read, and so you don't need to have the directories in which the datafiles reside present in your new host. However, the directories references in the parameter files must be present. From your transcript,

DB11G.__oracle_base='/u01/app/oracle'#ORACLE_BASE set from environment
*.audit_file_dest='/u01/app/oracle/admin/DB11G/adump' 
*.control_files='/u01/app/oracle/oradata/DB11G/control01.ctl','/u01/app/oracle/oradata/DB11G/control02.ctl'#Restore Controlfile
*.db_recovery_file_dest='/u01/app/oracle/fra'
*.diagnostic_dest='/u01/app/oracle'
*.log_archive_dest_1='location=/u01/app/oracle/archive_logs'

You may find this chapter of the documentation useful: http://docs.oracle.com/cd/B28359_01/backup.111/b28270/rcmdupdb.htm#i1006474

I cannot say for sure why RMAN behaves in this way, but as a workaround you can edit the resulting script within the same workflow in EM before the job is created:

 ALLOCATE CHANNEL disk1 DEVICE TYPE DISK FORMAT '/disk1/%d_backups/%U';

This will ensure the backups are placed in the destination you specified regardless of RMAN settings in control file saved with CONFIGURE command.