We've spent some time trying to understand this anomaly, even re-running Sonnet 4.6 through our evaluations to see if that would bring down its scores... and it didn't. I don't know what they did differently, but it's basically Opus 4.6 with more temperature variability (some great responses, some less great, with an approximately frontier median response in agentic work specifically). It is smart, methodical and excellent at tool calling in our custom environments.
We now use Sonnet 4.6 for a number of internal use cases we wouldn't have considered otherwise.