But the compiler's output will be polluted with these false positives, making it harder to see actual errors. (Also, there's a compiler flag to prevent codegen on error, which comes in handy sometimes.)
We made the decision some months ago and Flow's ES6 support was better than TypeScript's (and we already have a lot of ES6 code).
We also have an established toolchain with gulp and browserify and babel, and again, at the time TS didn't play as nicely (vs Flow which just worked). Things are definitely improving in the TS world, and I keep tabs on it. The fortunate thing is that both Flow and TS' annotations are compatible, so it should be relatively easy to switch from one to another.
Whichever one you go with doesn't actually matter though. As long as you go with one of them you'll see a massive increase in productivity vs vanilla JS.
There are still cases where you'll need to sprinkle <any>. For example:
is valid JS, but the TS compiler will complain that `state` does not have a member named `bar`.