The JVM is an advanced, mature JIT compiler. PyPy's generated JIT compilers are not as mature. As a result, the JVM does many of the things in the article and more. From what I see, the benefits of Clojure targetting PyPy would be exploring the performance advantages of very experimental work. Keep in mind, you'd be losing one key advantage of the JVM, which is the rich base of libraries written in java. I believe a main motivation to target different platforms would be because you want to leverage resources available only while on those platforms.
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