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 was more defending being a pedant about whatever coding standards your team agrees upon rather than any specific PEP-8 standard.
It is no problem to increase PyLint's line length limit if your team wants to use something other than the PEP-8 79 character limit.