I count Warmech since you would have to be incredibly lucky (or unlucky) to run into him.

I've always had a hard time counting summons as optional bosses cause I never really saw there being a choice. I "gotta catch em all" or something like that.

The Guardians in the final dungeon of FFIV also fall into this category.

I guess I would say Omega and Shin-Ryu from V to be honest. Especially since beating Omega really doesn't net you anything worthwhile outside of bragging rights.

VI also has this issue where the dragons are optional but really the Brontosaur in Dragon's forest is a much greater challenge to beat than most of the games enemies. So I always felt Brontosaur was more of VI's version of Omega or the Weapons.