@abravalheri happy to make changes! many thanks for noting this.
Rather than diverting the convo here - would you be open to creating an issue in our repo here: GitHub - pyOpenSci/python-package-guide: A guide to scientific python package recommendations curated by pyOpenSci i have a few questions for you about this and can show you what happened in a package i created as well 
@sinoroc yup - i think a nice working case for flit also is people making small modules for personal use. it’s light weight and quick to get up and running. Although, i wish it might make a directory structure for someone if they wanted to start from scratch too (minor and maybe out of scope). here is a blog post that i intend to publish soon about Flit - Learn About Using Flit for Python Packaging - HackMD just so you can see the interface.
what would be really cool if is some of these tools could just built upon each other extending functionality for various groups of users rather than rebuiliing similar functionality that is slightly different (if that makes sense). i don’t have a good solution this is just an observation.