Using function from enqueued .js file in theme in plugin?

Yes. Dependencies work across all of WP, it doesn’t matter where you enqueue your script. All that matters is that you define your dependencies correctly, and you’re doing that.

If, however, you plan to publish both the theme and the plugin as standalone versions, you shouldn’t rely on your plugin being used with your theme, and add the same script to your plugin (using the same name so it’ll only be loaded once by WP). If theme and plugin are only available as a combo, don’t worry about it.