The JACL reader is asynchronous, and so JACL can read characters from external sources (in-browser REPL, DevTools connection, websocket, experimental File API) without blocking the event loop and without relying on an external tool. JACL app artifacts will be created by dumping the Lisp image using a Lisp function.
Other than these technical differences, there seems to be a difference in "philosophy of use". I have the sense that the ClojureScript project does not emphasize or particularly support the idea of using self-hosted ClojureScript to build web apps.