To make a long story short, latency and throughput are two different metrics; that much is obvious. The important thing is to understand the difference between the two and their mutual relationship. Latency can be measured only between two different points in the system; There's no such thing as latency at point A. Each message has its own latency. You can average the latencies of multiple messages; however, there's no such thing as latency of a stream of messages.
Throughput, on the other hand, can be measured only at a single point of the system. There's a throughput at the sender, there's a throughput at the receiver, there's a throughput at any intermediate point between the two, but there's no such thing as overall throughput of the whole system. And throughput make sense only for a set of messages; there's no such thing as throughput of a single message.