The Python best practice: you do not need "correct directory structure" to start programming in Python--there is no boilerplate structure to create (and that would require a tool): REPL, Jupyter notebook in a browser, a single file (module) is enough in a simple case.

There is no single "correct directory structure" for more complex cases either e.g., a Django web app and Ubuntu's Appindicator would probably have different structures and it is likely that there are tools that create corresponding project skeletons such as "django-admin startproject mysite".

Usually, the packaging/deploying are not nice & neat and differ depending on your project, chosen platform--either you follow an example or you have to study a never ending list of incomplete/contradicting standards/semi-documented rules & conventions--it is unrelated to Python (even if tools such as Ansible, Salt are implemented in Python). Naturally, there are things that can be improved.

btw, reStructuredText is a great text format for documenting Python projects (it scales from a simple README.rst to a whole book). You can always convert README.md written in your favorite Markdown flavour using pandoc or a similar tool. Markdown is great for a short human-generated plaintext content common on Github, Stack Overflow.