Modules are easier to manage - they allow you to have multiple config's in either webpack/rollup and therefore you could have one for production, one for development, one for testing etc.
Using modules also has the added benefit of allows devs to more easily work on sections of code. This means version control is less likely to encounter issues as you wouldn't be working in the same file. @mevrael shows a great example of this. I could work on ModA and you could work on ModB and both commit - no conflict issues and jobs a good un!
I've just concluded the MVP of quite a large project myself, written in ES5, and am in the process of transferring it over to ES6 by utilising modules + import/export.