I'd wager that it's the TB/Undertow code running most of the time on that benchmark. On real-world benchmarks the difference is going to be a lot smaller. Not saying that you shouldn't run your JRuby apps on Torquebox - it's a great choice.
Since TorqBox/TorqueBox 3 is very new, I don't suspect it's being used much yet.
[1] https://github.com/TechEmpower/FrameworkBenchmarks/blob/mast...