Well, if you took the answer that you quoted literally, your configuration isn't getting loaded. The answer suggests putting the config in ~/.emacs.c/custom.el. That's a typo. The correct path is ~/.emacs.d/custom.el. The more correct answer is to put the config in the file pointed to by custom-file. The most correct answer is to never edit the custom file by hand. Instead use the customize facility.
- Run
M-x customize-group flycheck.
- Scroll to the bottom of the buffer and click on "Flycheck executables".
- Find the python executables you want to change. (Always use
python3 for Python3 stuff, even if you only have Python3 on your system. It'll save you headaches later.)
- Scroll to the top of the buffer.
- Click "Apply and Save".
- Boom. Your settings are saved in the correct "
custom.el" file.
Now, load up a Python3 file you want to use flycheck with. If it's not doing what you expect, check things with C-c ! v (aka flycheck-verify-setup.) Confirm individual checkers with C-c ! ? (aka flycheck-describe-checker.) Check the variables you think you're setting with C-h v. Cut-n-paste them from flycheck's website if you have to.
Don't worry about flake8's config file. It will properly cascade as you expect.
And, lastly, as @jenesaisquois suggests:
#!/usr/bin/env python3
import sys
print("# My message for the stderr", file=sys.stderr)
