As it is possible to skip EoC in progression it's difficult because if you haven't killed EoC yet in points of progression it'll still spawn naturally until you kill it, which means every time EoC spawns you'd either have to save and exit your world every time it spawns or wait it out until daytime where it despawns on its own, or just simply stay out of its reach at a certain distance.
Would also be a bit troublesome when facing mech bosses if it were to spawn naturally that way too upon engaging a mech boss fight.