When both were on version 5.1, there didn't seem to be any downsides to LuaJIT. Many Lua projects could benefit from it as long as they weren't trying to run on a platform that disallows JIT compilation (e.g. iOS or a game console).
However, now that LuaJIT is 2-3 language versions out-of-date, and has different best-practices (e.g. around FFI), it's almost like the two are different languages.