Object preferences are saved in each individual part file. Changing the site settings will not affect existing parts (this includes new files created from templates - the template is an existing part). If you create new parts from a template, open the template, change your settings as desired, and save the template. If you would like to test your site settings, create a new part using the "blank" template (it is the only one that inherits its settings from the customer defaults).
It does something, just not what you wanted. Setting the customer default options still has value; some dialogs (mostly drafting stuff) has an "inherit from customer defaults" option. Customer defaults were a much bigger deal before they introduced templates. Since most of the settings are saved at the part level, most of the changes you make these days involves editing the template file(s).