Glad to see Flask surpass Django, it's always been my favorite web framework regardless of language and forces users to learn their style of software architecture. I personally prefer MVC: https://github.com/esteininger/flask-mvc-boilerplate
I have interviewed plenty of flask and Django Devs, and usually, the Django Devs reply to some of my questions is usually "that's how Django does it"
That is a poor, poor answer.
Look at exploreflask.com for a great example on how to structure production grade flask applications. Read the flask docs, the later sections deal with the create_app factory function and how to use it. It is really good in that sense.
Agreed, but that's the beauty of Flask you can just pass around the request context.
Ideally request would be passed to view callables and would not be global. That is completely incompatible change so we will never see that I guess :(