Hi Sanjog,
The method you have use is correct you can exclude particular message there, those things will not be compared during CCR run.
Apart from that you can filter the it on the basis of Category too by method RELEVANT_FOR_COMPARE_APO.
You can use this method to filter particular SAP APO objects that you want to compare with the ERP objects. In addition, you can specify that only those objects that have an entry in the table /SAPAPO/CIFLOOKU (look-up information) should be compared. An object receives an entry in the table /SAPAPO/CIFLOOKU when it is sent to SAP ERP for the first time, or when it is created in SAP ERP. This prevents objects being displayed as inconsistent if they have not yet been transferred using transaction /SAPAPO/C5.
Regards,
R.Brahmankar