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I think there might be a fixed, constant overhead each time you call the Lua code, so the actual advantage within the Lua code is actually much higher. From the results with RB, it seems that LuaJIT also has a smaller overhead constant.
About the difference between AMD64 vs ARMv6 instruction set, one is CISC other is RISC, so the CISC will benefit more from the pure assembly components that were part of LuaJIT because more suitable instructions can be used to do multiple steps in one instruction. At least, that's my guess.