Do you mean running Vue by just adding a script tag to the page? That will still work because it's just using a precompiled/transpiled JS file, which will continue to be available as part of the package. FYI, React can also run the same way.
What are you talking about? Typescript is what the Vue source code will be written in, which is compiled to javascript when distributed and includes Typescript definitions for editors that make use of it.
Your code can continue to be written in regular javascript with whatever toolchain you want.
And Typescript is a fantastic platform for bringing strong typing to Javascript, it's a rather extreme comment to say you don't recommend it to anyone.
Why would you use flow with typescript? Also valid javascript is valid typescript, you can even have typescript's tooling lint your javascript with a jsconfig file.