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Not sure as I never use CFD Post - there should be some pre-built reports which includes mass flux. I post process everything in Fluent. The only issue in Fluent on interior faces is aligning the facet normals, as interior faces don't do this automatically. Sum of radial velocity * facet normal area should work too. 

For flow boundaries if you look at the mass or area average you can get a different result. For flux it's probably less of an effect, but for (example) temperature if you return area average you'll miss that the highest flowrate also carries the most mass so you can miss represent the mean temperature of what's leaving the domain.