The alternative to that of course is Babel. Which is standard JavaScript, mostly. Including the draft stuff that isn't ratified yet. But you don't have to use any of that if you don't want. And things like Flow and JSX, which are just plugins so again, you can take them or leave them.
The authors argument eventually distills down to a choice between TypeScript and Flow. He concludes that TS is the best choice because it has the momentum, but that's a false choice. The choice is between Microsoft's TypeScript transpiler and Babel.
If you use Babel you can choose to use Flow, but if you use TypeScript you lose out on everything else Babel has to offer.
And outside of the .Net+Angular world, Babel has all the momentum.