I use flow as well at the company I'm working for. I found lightweight setup that works surprisingly well for me. It started as experiment to use types in comments. There is no transpilation phase at all, just pure js with types in comments. All my projects use simple npm test "eslint . && flow check && jest" and there are no prepublish hooks, no manglings, no source maps etc. It means you can edit linked modules in place and get instant feedback. The workflow is very fast and non intrusive. It looks like this [0] or this [1] etc.

[0] https://github.com/appliedblockchain/parser-combinators [1] https://github.com/appliedblockchain/helpers