$auto_prefix_models is used only in Model::factory. When I use has_many, Paris tries to use class name without namespace prefix to determine the table name for the joined entity.
It can be fixed by changing the first line of the has_many method from
$associated_table_name = self::_get_table_name($associated_class_name);
to
$associated_table_name = self::_get_table_name(self::$auto_prefix_models . $associated_class_name);