Hi Anoku,
Hope you are doing good.
Just another point here. The ARFC 2 model should be used by new applications (custom or otherwise as http://scn.sap.com/docs/DOC-2594 states), but components, ESS/MSS still uses the old ARFC model.
So until they migrate to the new model, the JCo destinations for these should be maintained in the Web Dynpro Content Administrator instead of /nwa -> destinations for ALL SAP releases.
So it depends on the application that you are trying to configure.
Thank you!
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Kind Regards,
Hemanth
SAP AGS