Javascript is actually probably the fastest scripting language out there, because it's had the might of Google working to optimise it with the V8 engine and Crankshaft. It literally compiles it to machine code. I've read Google engineers quoting it as comparable to unoptimised C code (as in, maybe two or three times slower than optimised C, rather than ten times slower or worse).
Python is only interpreted as far as I'm aware, and Lua appears to have a JIT, but I can't see it being so much faster than Google's V8 to be worth switching to. Besides, the plan is for the EXE runtime to all be written in optimised C++ - to make Javascript plugins work in an EXE runtime one of the things we'd have to do is write a full virtual browser emulating the presence of the DOM, window, cookies, URLs, canvas, contexts, Javascript library functions, and so on. That's kind of a ridiculous thing to do for a C++ runtime, especially when C++ extensions would be faster and more compatible anyway.
So yes, it's a shame that extension developers will probably have to rewrite extensions for other exporters, but that's the way it has to be done.