Advantages of teaching basic javascript through typescript
You mention that you are already using ES6, which suggests that package management and complication are not really barrier, though I would expect that many reading this problem are not setup to ensure node and npm are installed and/or may have access to git/ssh protocols for fetching dependencies or projects. So, the first thing I'd point out is that for some readers, compiling TypeScript could be a barrier that reduces is teaching value.

The second and more relevant point is that JavaScript is dynamically typed language. There is value in tools like Flow and TypeScript, especially in production systems, but there is also a great amount of value learning how to program in a dynamic type system. If you're already teaching Java, there are few better choices to teach strategies, advantages and disadvantages to dynamically typed systems. Some students will prefer that type of programming over strictly typed languages.