Fixed Bug #66218 zend_register_functions breaks reflection

Functions registered using zend_register_functions instead of zend_module_entry.functions are not seen on reflection.

Ex: additional_functions from api_module_entry.
Ex: in CLI, dl, cli_set_process_title and cli_get_process_title

Note:
- also affects functions overrided in extension
  (should be be reported in extension, where overrided, not in original extension)
- also allow extension to call zend_register_functions for various list
  (instead of having a single bug list)