Flow + OCaml is a great example of this approach failing IMHO. I ran into tons of issues that were difficult to debug myself, and things like the regex format and config file conventions being different were also problematic. Compile times are also annoying.

Something undervalued is the debuggability of using a single language. There are so many times I need to debug some tooling, and being able to to just open the stack trace and place a breakpoint/console.log is incredibly valuable. I do it all the time for webpack/babel.

Having to switch to a new toolchain to debug something is tedious, and often impossible to reach the same convenience of JS-based tools.

I think the future is taking small pieces of JS-based tools and adding native extensions to speed up parts of them.