Considering you can run bytecode-only Python, it would be weird if Pypy's JIT only worked from source.
Beyond that, they're apparently implementing Clojure on top of (in) Python, so they won't get the JIT for free (the interpreter code will be JITed, but the Clojure code won't be unless their runtime compiles to Python bytecode which does not seem to be the case). They'd get it for free if they implemented a Clojure in RPython as well, but would leave the Python ecosystem behind.
> clojure-py is an implementation of the Clojure language in Python, compiling Clojure code to bytecode for Python’s virtual machine
Which means both the compiler (mostly an AST walk from the look of clojure/lang/compiler.py) and the Python bytecode it produces should benefit from PyPy's JIT.
Edit: Nevermind, just read the project readme[1] where they explicitly mention targeting PyPy as a goal.
[1] https://github.com/halgari/clojure-py