How do I prevent a ClassNotFoundException when calling Java interop from Clojure in a JNI-created thread?

Question

I have a project that's using Clojure + JNI in order to access some operating-system specific APIs. The native code in this process runs some of its work on background threads, and when doing so occasionally calls a Clojure function. I quickly learned the importance of calling javaVm->AttachCurrentThread on these background threads in order to be able to call the Clojure function in the first place, but now I'm hitting another roadblock.

It looks like any Clojure function that uses the clojure.lang.RT library fails to run in this setup, with an error that says Exception in thread "Thread-3" java.lang.ClassNotFoundException: clojure/lang/RT. A great example are the array functions (e.g. alength and friends), which are used to pass data back and forth between the native side and Clojure side.

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Edit: I've put together a condensed reproducible example in this repository: clojure-jni-threading-example. It appears that the error is related to type inference; the following Clojure excerpt leads to the error:

(defn alength-wrapper [x]
  (alength x))

(JNIClass/callFromJNI
 (reify JNIFunctionClass
   (callMe [this]
     (let [c (byte-array 6)
       (println "c" (alength-wrapper c))))))

The error can be prevented by added a type hint:

(defn alength-wrapper [x]
  (alength ^bytes x))

I also tried to reproduce this error by creating a separate thread in Clojure when calling these functions (e.g. using future), but of course that works. This suggests there may be some initialization step that I'm missing when using JNI.

How can I prevent this error from happening so that these Clojure functions can be called from JNI background threads, without needing type hints?