I think the best way to handle these messages that should have the _t() method applied to them, is to create a patch and a ticket for them. This ticket would probably also include an entry in cms/lang/en_US and your chosen language file...
The translation would look something like this
FormResponse::status_message(_t('CMSMain.SAVEDSITECONFIGURATION','Saved site configuration'), "good");
In the meantime, there's not much else to do but manually enter the replacement code in your core, I guess :-(