No wonder the world is running towards Python and serverless as fast as they can...
Also, most of the things you complain about are not Java: they are the fault of JEE (aka J2EE) and "app servers."
The only benchmark where it's faster is the one involving threads, which makes sense. CPython definitely has multi-threading support, but it also has the Global Interpreter Lock preventing threads from actually executing bytecode at the same time. Jython doesn't. People have written patches that successfully remove that GIL, but those patches make single-threaded performance worse and thus haven't been accepted.
The py3 version is calling numpy which calls a highly optimized C library. So this benchmark suite is worthless. They failed to warm up the JVM hotspot compiler, and they are comparing interpreted Jython with a highly optimized C library called from Python3
The lack of a warmup phase is confirmed by the raw command line and output logs on various benchmarks. Amateurs. This is a highly misleading set of results on multiple levels.