Add the babel-plugin-react-intl to your create-react-app app via react-app-rewired.

npm install --save-dev react-app-rewire-react-intl

In the config-overrides.js you created for react-app-rewired add this code:

const rewireReactIntl = require('react-app-rewire-react-intl');
/* config-overrides.js */
module.exports = function override(config, env) {
 config = rewireReactIntl(config, env);
 return config;
}

To pass options to the Babel plugin use the third argument, it passes straight through to the plugin:

config = rewireReactIntl(config, env, {
 messagesDir: './build/messages/',
})

See the available options in the babel-plugin-react-intl documentation.