Beiing HRE emperor and managing it in order to form a single country should be as hard as doing Three Mountains. The Emperor is already for more wealthier and powerful than it ever was in history. The Emperor do not need a magical protection, it's already strong enough to stomp down France, PLC and the Ottomans. I'm against magical border, you can truce-break an alliance, but you can't wage war against two OPM because "you're already at war with the emperor". If you are at war with a country, and one of its vassals is on scutage, the vassal is not part of the war, but you can still declare another war on him. It should be the exact same thing for attacking the HRE, as the overlord get the "reconquest CB", the emperor get the "liberate imperial territory CB", it should be enough.
I’d take the opposite tack - you shouldn’t be able to declare war on a scutage-vassal while at war with their overlord. It’d an exploit.