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