php.ini opcache path for multiple websites with shared code base
If I understand your question correctly, I believe you can use ini_set() in your settings.php files if your multisite required different PHP ini configurations.
Example 1a:
// @file docroot/sites/default/settings.php
ini_set('opcache.file_cache', '/path/to/opcache/default');

Example 1b:
// @file docroot/sites/my-other-site/settings.php
ini_set('opcache.file_cache', '/path/to/opcache/my-other-site');