I've an idea that might make fighting superbosses completely optional yet actually making sense and reinforcing the story.
An antagonist(also the final boss, I abbreviate it as F

is powerful and has many minions. He aims to be as powerful as possible at all cost and he also wants to prove how powerful he is.He feels that the only way to prove is to firmly control the whole world and eliminate any opposition via raw power(such as total destruction). He and some of his minions creates an extremely powerful prototype(with mass production if it's successful) with the state of the art equipments, knowledge, abilities, AI(aiming to assist its user in order to make it as powerful as possible and it's still supposed to be controlled by its user) and some other technologies and he thought it's under his control, but it turns out that it's actually more powerful than him and he can't control it due to its overpowered AI(due to his arrogance and mistakes made in creating it). As it posed him a serious threat and he can't defeat it(or will be too badly injured and lose too many minions even it he can), he decides to halt the project and seal it temporarily, although still losing some minions in the progress. That prototype can't break the seal even though it's more powerful than the FB.
However, the FB insists that he can control that prototype eventually if he's powerful enough(or if he can finally write and finish a program that forces the AI of that prototype to obey its user), and if he can really control it, the world will be over instantly. Of course, the threat posed by the FB is still too large to be ignored even if he can't.
Knowing all these, the protagonists can either defeat the FB and let that prototype superboss to be sealed forever, or break the seal and defeat that prototype superboss, gaining extra power, information or other bonuses before facing the FB himself. Of course the seal has to be well hidden and the FB has to believe that no one can break the seal without him and he won't even check it before he decides to break it with himself(and it won't trigger an alarm if it's broken), or a plot hole will probably exist.
And if the protagonists break the seal but didn't defeat that prototype, it may defeat the FB itself but it may also become an even bigger fear than the FB, even though that prototype may not have such agendas.
Or if the protagonists managed to write and use a program to force the AI of that prototype to obey them(but they still need to fight it), causing it effectively under their control, they can even use it to fight the FB.
Maybe the protagonists can even break the seal and defeat that prototype after the defeating FB and probably also watching the end game credits, and players can treat this superboss as a post game bonus.
Now that prototype superboss is optional but more powerful than the FB and its battle is also more difficult than that of the FB, yet the existence of that prototype actually reinforces the story, by at least the below ways:
As the main objective of the protagonists is to neutralize the threat posed by the FB and defeating that prototype erases the current known worse case(the FB can finally control and release that prototype and the world is instantly over), defeating it is related to the main objective even though it's not the only way and it's supposed to be the optional and hardcore way(and that prototype may serve good or bad purposes later if it will ever be released by the others).
If defeating that prototype yield bonuses like extremely powerful moves, items, equips or extremely useful information like a FB's weakness that prototype couldn't exploit itself but can be exploited by the protagonists, defeating that prototype makes defeating the FB easier. Or maybe taking the reverse path, right before that prototype is sealed, it might have secretly casted some hidden spells weakening the FB's power without even being realized by him(to reduce the chance for him to be powerful enough to control that prototype again), and defeating that prototype voids its spells casted to the FB, causing him to be more difficult to defeat. Of course defeating that prototype has to yield some other rewards in this case.
Or defeating that prototype yields some extra information about some details of the project behind it and these details is completely optional to the plot(of course they still have to conform to it). These details may be similar to easter eggs.
Also, that prototype superboss being stronger than the FB makes sense as it's like a super weapon that is created by its intended users and is intended to the more powerful than its users yet controlled by them. As long as the FB can indeed control that prototype, it'll be a part of that FB's power. But if the FB can't control it, it won't be a part of that FB's power and in this case, it'll be more powerful than the FB, making it a superboss.
I don't know if this idea makes enough sense or is possible to implement well enough to make superboss really reinforcing the story and I don't know if any famous RPG uses this or something similar or this has been ridiculously overdone, but that's my try on this topic
