The mentality of someone who thinks that an 89-character line that ends with " # noqa" is better than the 81-character line without that ending because now it passes flake8 is one I'll never understand.
I don't disagree, but keep in mind that on the large codebase you want to avoid false negative in term of pep8 errors.. I.e. if every time you build you see 100s of errors, you start to ignore those.
https://www.python.org/dev/peps/pep-0008/