RF PDSCH throughput is widely used one in RF benchmarking purposes and basically, APP layer throughput is used for User perceived throughput from Session setup start to Session End.
And moreover since in 5G we have data divergence at PDCP for ENDC, we will get the performance of each radio interface for 5G & 4G from Physical throughput (PDSCH/PUSCH throughput) and due to header additions the tpt will be App layer < PDCP < RLC < MAC < PHY.