I agree that 'William I the Conqueror' is quite wrong, and some punctuation, either commas or brackets, is needed to clarify the two styles. You also couldn't say 'William II Rufus'.

Or William the Corn-curer as may old Dad always says; him and Edward the Confectioner.

As an encyclopaedic head-word it's a quandary. Even worse when other languages require translations: Mehmet II Fâtih (the Conqueror), or Süleyman the Magnificent, who in Turkish is not called Magnificent but Kanuni 'the Lawgiver'. Not sure what you use for a head-word for these.