With Flow, the type annotations are just stripped away, none of your Flow code affects runtime code.
This is not so with TS since you have things like Enums, which will be compiled into objects and are part of your runtime code.
If you write type annotations in Flow, they're stripped away.
There's no difference. TS has some additional features which are purely optional that don't get purely stripped out, but you're not mandated to use them.
In my eyes, it's a philosophical difference between the two, Flow can be more easily integrated into an existing codebase by just adding //@flow at the top the file and has no features which can affect runtime code. Whereas TypeScript tries to be a different language altogether that uses a new file extension, adds new features, and has its own compiler.
When you can implement a tool like this using TS, let me know https://github.com/flowtype/flow-remove-types
Enums are a fair point, those aren't in the ES specs (though I suspect at some point they will be). However, they're an incredible addition and they really are just syntactic sugar for a more complex type of object.
BTW, typescript supports jsdoc-style annotations, and --allowjs even lets it typecheck javascript code. It also supports more, because nobody actually only wants those things; they're not that great on their own.
You might not think the differences is a big deal, but affecting runtime code is a pretty major line to cross. Not that there is anything inherently wrong with that, but at that point it becomes a different tool, in my opinion.
enums are a tiny, extremely useful and extremely optional part of the language and they don't warrant this label of "philosophical difference", IMO.
That's what Typescript is. Type annotations don't change your code, they're stripped away by babel at compile time. In fact, by default, tsc does compile TS code which fails typechecking, into valid JS code (which will likely error when you use it at least in some circumstances, but can run just fine).
Typescript is a clear superset of JS, so there's no actual logical changes or even syntactical changes done by the compiler. However, you may be confused by the often-used "compilation target" features of babel (and tsc), which is that you may write ES2018 code, target ES5, and have your ES2018 syntactical sugar be turned into ES5-compatible code. This is entirely opt-in, and not related to typescript (other than the fact that Typescript is always compatible with the latest ES spec, so you can use any legal ES2018 syntax in it).
Hope that clears it up…