"Boss Fight" Ideas

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Well, actually, such kind of "boss fight" are possible, even without ruining the immersion/atmosphere. For example, if you encounter some powerful enemy in the location (which is, of course, justified by the story), who haunts you in this location without giving you a rest, you could use the tools and aspects/features this location provide to kill/get rid of him. Like locking him somewhere, or pushing into the pit or luring into some kind of mechanism to crush later. I can see how it could be consistent within the gameplay. Conception is not a problem , the execution/realization is. It is hard, despite the fact it sounds so easy.

I see what you're saying, but IMO, giving the player any way to fight back against an antagonist just takes away from the horror. Sorta like Penumbra: Overture; once the player figured out they could kill the enemies, it was no longer scary, it just became a (to quote the developers) "hack n' slash". If a boss fight were implemented, the players focus will undoubtedly get pulled away from the environment and becomes centered on that one goal, thus reducing the horror experience.

@OP:
You shouldn't rely on gimmicks like a boss fight to try to make your story unique; Believe it or not, just the story alone can be powerful enough to provoke a wide array of emotions in the end. For example, the ending events to Justine: If they had no story behind them at all, it would of been a lot less immersive. It is because the unexpected ending, and all of the events+story leading up to it, that it was so powerful.

It's a myth that the ability to defend yourself unerringly relieves tension. My immersion was never broken while playing Overture and I killed all of the dogs. It's still very finicky to kill them and the weapons are unreliable. Sneaking up on your enemies before they sneak up on you has real animalistic feeling to it, and it at least made me very nervous. Black Plague and Amnesia are scarier no doubt, but Overture is not a hack 'n' slash. At least that's not the experience I got. Also, it is possible to have bosses without breaking immersion and I think Frictional should seriously consider this, because you don't need to implement button-mashing combat mechanics and have trial and error for it to work. There do exit bosses that require only strategy and puzzle solving and these types of encounters can be quite effective. Here's an example:

http://www.youtube.com/watch?v=nXjAAF88-Zw#t=37m36s

Though this was not exactly scary it made me uneasy and I found it to be a brilliant moment (not a very good game though if you were interested in playing it).