One thing to note about ahistorical de jure empires:
The game is designed around the assumption that every de jure kingdom has a de jure empire title. It doesn't need to be creatable, though. Why? They are used for more than just a title that a player may hold. They are used to group together related kingdom titles (as in, kingdoms that a ruler might plausibly have territory within) for a variety of purposes, incl. things like calculation of effective liege levies based upon de jure territory or using the empire titles as geographical guides for conquest for the Tribal Invasion, etc. etc. It's actually really important to stick to the model of having a de jure empire title defined to cover every province on the map. They, of course, don't have to be possible to create, though.
It would be really nice if Paradox would code their 'de jure empires' map mode so that deactivated empire titles (all titles have an 'active' flag-- all holy orders, e.g., start deactivated and are then activated later by event) just appeared as the 'dark grey' of 'no de jure empire' for display purposes. It would end a lot of confusion and let us organize the titular structure of the map optimally for the engine w/o introducing any ahistorical empires into the game. Unfortunately, even if a de jure title is deactivated, its color appears on that stupid map mode, causing a lot of confusion.