One comparison I'd make is between the Hellboy comics and the Hellboy movie:
In both versions, the story revolves around an evil sorcerer trying free an elder god-type thing, which once free will end the world.
In the movie he succeeds, but Hellboy stuffs the elder god back in it's "bottle" before it's able to commence wrecking things.
In the comics, not only does he fail, but it's heavily implied that if he'd succeeded, there would be no stuffing the elder god back in the bottle, no matter how powerful or hooked up you were. This foe, as Gandalf would say, is beyond any of you. If it gets out at all, that's game over, right then and there.
So why the difference? Well, the comic is built heavily on suspense and atmosphere inspired by old gothic horror films and Lovecraft-type stories. The movie is built on action and a more colorful Marvel-ish conventional superhero type storytelling. The difference is one is all about the anticipation, and the other is all about the climax.
Coming back round to games: in a survival horror game having the giant robot, elder god or what have you looming over ones head throughout the game can be the "meat" of the experience. You're not supposed to want to fight it, you're supposed to dread it. If you're wanting to fight it, the game hasn't properly done it's job of scaring you with it. Letting it out can easily be the failure state for the game, and you don't need it as a boss monster. Depending on the gameplay style, you may not need a bossfight at all, just a boss puzzle or some kind of marathon challenge or something instead (example: Penumbra Overture). If you do need a bossfight, you can sub the dragon for the elder God: fight the prick who's trying to summon it, and if it's a well made fight, it won't matter that he's not the elder god itself (example: Amnesia TDD).
An action game though is all about fighting, so the player spends the game expecting a big damn climactic fight. You don't watch a Van Damme move and not expect it to end with a 10 solid minute face kicking contest. You can't spend all game pimping up what is so obviously the final boss only to not fight it (examples: Borderlands 2, Jak and Daxter).
Thing is, a lot of major horror games basically play like rebalanced action games, thus necessitating a boss fight even though they're ostensibly not action games (example: Silent Hill series, Dead Space series). Not having the elder god wake up can easily work, but it needs to be in a game where puzzles, investigations, evasion, sanity, etc are the majority gameplay focus. In any game where combat is your #1 mode of problem solving, even if you're at a crippling disadvantage in combat, the player's gonna expect a bossfight, and you've spent the whole game telling the player "this is the top enemy", so it kinda has to be that.