For reference in case someone else is experiencing similar "issues", if a path is provided when running pint, all excludes inside the pint.json file will be ignored. Therefore with the above example, if vendor/bin/pint is run on its own, bootstrap/cache will be ignored.

Reference: https://github.com/PHP-CS-Fixer/PHP-CS-Fixer/issues/2956#issuecomment-319713451