I also like https://github.com/svenstaro/flamejam/ as a good example of Flask architecture. It's simple and maintainable. I wrote a 4k+ loc app using a similar pattern and it still remains quite easy to handle.
I'm the author of that so if anyone has any questions feel free to shoot. Generally, the project is quite old but I still build flask application in quite the same manner as that. You can see the project running at https://bacongamejam.org