LuaJIT is a tracing JIT, which means it can re-optimize itself to better suite the data passed through the execution environment, however, LLVM is a static JIT, and thus will just generate the once-off best-case machine code for the corresponding source, which may leading it it loosing performance in tight loops or bad branch misspredictions.
The actual LuaJIT VM is also highly optimized, threaded, machine specific assembly, where as LLVM uses C++ for portability (and other reasons), so this obviously gives LuaJIT a huge advantage. LLVM also has a much higher overhead than LuaJIT, purely because LuaJIT was designed to work on much less powerful systems (such as those driven by ARM CPU's).
The LuaJIT bytecode was also specially designed for LuaJIT, where as LLVM's bitcode is a lot more generic, this will obviously make LuaJIT's execute faster. LuaJIT's bytecode is also well designed for encoding optimization hints etc for use by the JIT and the tracer.
ignoring the fact that these are two different types of JITs, the whole comparison boils down to LLVM is focused on being a generic JIT/Compiler backend, LuaJIT is focused on executing Lua as fast as possible in the best way possible, thus it gains from not being constrained by generality.
