Hi,
For instance in your example of clients-type.php you can remove our code by removing the action from the hook below
add_action('init', 'clients_register');
So in your functions.php of the child theme you should remove that action and add a new one using your custom function that should be a copy of the code inside clients.type.php but with different function names to avoid any conflict.
remove_action('init', 'clients_register');
add_action('init', 'custom_clients_register');
Regarding the page builder, I’m not seeing any way to overwrite the code, will check with my head developer.
-Rui