Clojure always must be handed the program counter from Java, the JVM can't load right into Clojure. So there's a few ways you can do it:
1) With a gen-class
2) From an already bootstrapped REPL
3) With clojure.main
4) With the Clojure runtime (RT.java)
5) With the Clojure Java API (https://clojure.github.io/clojure/javadoc/clojure/java/api/Clojure.html)
6) With popular tools such as Leiningen and Boot
Any time you want to run some Clojure code from Java, you need to do it with one of those mechanisms, and you cannot run Clojure code without going to Java first.
The issue is that, not all mechanisms hand over execution with an equal context.
#1, #4 and #5 all hand over execution from the context that the Clojure runtime executes in. That means that you get a minimal context running inside the "clojure.core" namespace. No binding is setup, and ns points to "clojure.core".
#3 and #6 seem all to hand over execution with a similar context, but one that's different from #1, #4 and #5. That is, they set common bindings such as ns, and set the current namespace to a freshly created namespace generally called user which has clojure.core referred in it. Meaning that code executed from #3 and #6 will be able to set common bindings and won't interfere with the clojure.core namespace.
#2's context will depend on how the REPL itself was bootstrapped from Java. In most cases, clojure.main, lein, boot, it will be similar to #3 and #6.
I believe that it would be healthy for Clojure to standardize the execution context when bootstrapping Clojure from Java, so that all above mechanism behave the same. This will make it so that all code will run equally from all bootstrapping mechanism. This is not currently the case, since missing bindings and the clojure.core current namespace can cause certain rare scenarios to fail under #1, #4 and #5, but work under #3 and #6.
To not break backwards compatibility, it would be better to enhance #1, #4 and #5 so that they also set common bindings and change the current namespace to a fresh user namespace with clojure.core referred in it.
Initial discussion on the mailing list: https://groups.google.com/forum/#!topic/clojure/6CXUNuPIUyQ