It is no surprise that the benchmarks on the LuaJIT website are going to show it ahead of PUC-Lua, is it? In truth the performance comparison is a bit more complicated than that. :)
For a pure Lua comparison LuaJIT is typically going to beat Lua by a large margin. For code that can be JIT compiled you might see ~10x performance improvements and for code that doesn't you might still see around a ~2x improvement because the LuaJIT interpreter is written in hand-crafted assembly language (PUC-Lua sticks to portable and standards-compliant C90).
But things get a bit more complicated if you add foreign C code into the mix. Under LuaJIT, the JIT compiled code that uses the LuaJIT FFI interface is the fastest, but interpreted code using the FFI is slower than interpreted code using the traditional Lua-C interface, and can even be slower than PUC-Lua using the traditional Lua-C interface. This means that when you are using LuaJIT you need to be very careful to make sure that your code is the sort of code that can be JIT compiled. If you hit a "not yet implemented" feature you can have a big performance degradation.
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Nevertheless, Lua 5.4 has brought significant performance improvements compared to Lua 5.3, specially in integer operations (including for loops). Another big change was that the `#` is now faster. For example, on my machine the following loop runs in 1.96 seconds in Lua 5.3, in 1.26 seconds under LuaJIT, and in 0.96 seconds in Lua 5.4
local a = {}
for i = 1, 1e7 do
a[#a +1] = i
end
print(#a)
The new generational garbage collector is also a very big improvement. I've measured a 1.5x speedup on some GC-dominated workloads, where the final result was that Lua 5.4 would even edge out LuaJIT, which is still using the old incremental collector.