I've noticed an overreliance on throughput as measured during 100% load as the performance metric, which has resulted in hardware vendors "optimising to the test" at the expense of other, arguably more important metrics. For example: single-user latency when the server is just 50% loaded.

That’s more than fair.

In the system I’m most familiar with, however, the benefits of hyperthreading for throughput extend to the 50-70% utilization band where p99 latency is not stressed.

Or p98 time for requests. Throughput and latency are usually at odds with each other.