Also extend documentation of 'missing-reference'.

In Python 3, the default encoding of source files is utf-8. The encoding
cookie is now unnecessary and redundant so remove it. For more details,
see the docs:

https://docs.python.org/3/howto/unicode.html#the-string-type

> The default encoding for Python source code is UTF-8, so you can
> simply include a Unicode character in a string literal ...

Includes a fix for the flake8 header checks to stop expecting an
encoding cookie.

The form is less verbose and more idiomatic for Python 3 only code.

https://docs.python.org/3/library/functions.html#super