After some reading and some conversations I believe the answer is that the ExecutionEngine essentially executes code as if it was native C code. Which means if you wanted to execute lua/python/javascript code ontop of llvm you would need to actually send the bitcode for that runtime. Then the runtime could parse and execute the script as usual.
As far as I know none of these runtimes have the ability to compile their script directly into llvm bitcode (yet).