Wouldn't that make the HRE completely unformable as well (as the title would no longer exist)? Is there a way to remove it from the emperor, so it just isn't a de facto nation in the game?
Edit: Slightly off-topic, but looking through that file, I see the regnal name listings for the Papacy and Ecumenical Patriarchate. If I added that to another title, would rulers acquire regnal names when they attain the title? I'd test it myself, but it seems like wasted effort when someone already has...
Edit2: Well, I answered my original question. I went into history\titles\e_hre and changed to holder=0 as of 1054 (when the last emperor who reigns entirely before 1066 dies). Now it will not appear, unless some German gets powerful enough to form the empire (which is unlikely and also too awesome to prevent).
I'm also mulling some way to make the post of Emperor exist but be borderline powerless, as it was for most of its existence. For example I could allow it to exist even if holder has no land, and give it to some landless guy (who then has power to change the crown laws but nothing else), but because it's elective (which I'm not prepared to change) the title would start falling into the hands of powerful dukes and rolling their lands together. And to stop that I could drop it down to Duke-level, but it seems a bit wrong to have an Emperor only have a Duke title.
Hmmm...