The TS community is far, far larger and more active than Flow, and I'm not sure eliminating Flow would make much difference. Facebook would certainly continue to use it instead of porting all their code to TypeScript.
The downside is for React developers. I am a React developer. I would like to benefit from the larger ecosystem of TypeScript: better availability of type defs, better editor support, more help on stackoverflow, etc.
But there are also benefits (for a React developer) of using Flow. For one, create-react-app has built-in support for Flow but not TypeScript.
The answer to your question "What are the downsides of competing standards?". For the same reason we try to standardize on other aspects of the JavaScript language and ecosystem when new things are added. Having 3 different ways to do promises would be a pain, so the community created a single standard way to do it.
The TS community is far, far larger and more active than Flow, and I'm not sure eliminating Flow would make much difference. Facebook would certainly continue to use it instead of porting all their code to TypeScript.