The problem is that you're assuming that the jump scare has to take place, which it absolutely doesn't. And when it does, it does not have to be a cheap scare such as a monster jumping out at you. The idea is to create the possibility of a jump scare, not the jump scare itself. You can go a long way without ever using a single jump scare, as long as you're able to establish that it is a possibility and it is absolutely something to fear.
For example: Imagine you're in an empty house. Lights flicker on and off, you investigate the house, you hear a lot of strange noises or footsteps from around the house. The game has somehow established already that you're in danger and capable of dying, you're powerless against the evil force. You're always on edge because of what might happen, but you manage to get through most of the house, except for one place...A long hall with no doors, except a bunch of stairs leading to a pitch black attic. You expect that something horrible is going to happen, you fear that something is up there and going to murder you, you feel the dread and fear build up in you with every step you take. THAT'S the greatest thing about jump scares, not the jump scares themselves, but the possibility of one. You could enter and exit the attic without anything ever happening, as the only requirement is that you never stop feeling that danger might pop up from behind every corner and that it is actually something to be feared (Something which Amnesia: A Machine for Pigs tremendously failed to do).
The key is to make the player scare him- or herself, not to scare him with jumps. Sound familiar? Exactly, it's the kind of horror everyone praises, without realizing that Jump scares can absolutely be a part of this.
And again, jump scares don't have to be monsters jumping at you screaming "ABLOOGIEBOOGIEBOO". They could be doors shutting behind you as the lights go out, a monster banging against a door you just closed (and thus the game warning you that you have to hide), a loud noise coming from right behind the door you need to get through. Jump scares are simply sudden grabs of attention that could result in people (not merely physically) jumping and can be used at many different intensities (as long as it's loud and sudden enough to make people "jump". It's not as much the monster jumping, but the player). Simplifying jump scares to loud and sudden in-your-face things is limiting the concept. People usually label this as atmospheric horror, but there is a huge overlap between "jump scares" and atmospheric tension. The modern definition of the word "Jump scares" is mainly due to the fact that most horror games only use the of monster-in-your-face kind of implementation
Even games that get lauded for their great horror, such as Amnesia (and even earlier SH to an extent), actually use quite a bit of jump scares. The key is to realize that they're a tool and must never be the focus of fear. Create fear through sound, atmosphere and gameplay, but only ever use the EXPECTATION of regular jump scares to intensify that fear and tension. Other than that, they use environmental jump scares to give context to both the world and area around them and to the atmosphere and situation at hand. The use or lack of use (and combining this with area/room design) is done to set up a mood (feeling safe in a RE save room or instead feeling immense stress or dread because an amnesia monster is suddenly banging on the door and trying to enter the room) for every given moment and this way they manage to make the players feel exactly what they want them to feel at any given time. We don't have any control over what we do or feel because of the mind games these devs play on us, which adds to the overall theme of hopelessness and despair.
Whew. Hope that my gibbering somehow makes sense.