Please summarise the discussion in the issue you've referenced as far as it's relevant to Flycheck and elaborate why we need to drop standard input for phpcs. Ideally, try to produce a minimal example where phpcs behaves different as expected with Flycheck.
it tells to phpcs to exclude that rule when the path of the file being checked match the patterns.
So, if you are checking files under src/ (which are almost all in a cakephp project and most other frameworks) and you call phpcs with file path it won't apply that rule, and you'll see less errors.
If you call phpcs with STDIN it can't know where the file is, so it applies all the rules, resulting in an incorrect list of errors.
I hope it to be understandable, my english is really bad.