You can't do what you're suggesting to the degree you're hoping for in the way you want
This is a frame challenge.
In many ways the human body is remarkably resilient. Somebody smacks you on the arm with a stick. Flesh, muscle, all kinds of things move around leading to bruising, damage, and pain. Maybe someone jovially taps you in the tummy. You lose your breath, but no real harm done, and everybody starts laughing a bit later. You get on a roller coaster or some other ride and get spun around, not just playing with your inner ear's balance, but actually jostling you something awful! You stagger off the ride, proudly proclaiming that you want to go again.
It seems like these are the kinds of experiences you're looking for. The problem is that during transport it's irrelevant what happens. That's all energy transfer. There's no feeling or comprehension. It's the period of the event that's explained using technobabble to justify what happens next.
During reconstruction of the body whatever happened during the transmission phase (and, much more likely, what's happening during the reconstruction phase. We'll get to that in a moment) is made physically manifest. But you can't change too much of the body. The "jostling" that happens during a roller-coaster ride or a tilt-a-whirl is not what's happening here. This is more like stirring pigment into paint. Once you've stirred pigment into paint you can't get the original color back. It's dead.
And that's your basic problem
You want people to feel weird about an experience but the process you appear to be relying on is a physical process that will result in dead people. You don't have a period of time where flesh is compressed or the body is moved around. All you have is the aftereffect of something that's (at best) interpreted that way. Otherwise, you have dead people. The damage caused by that stick to your arm is happening in a fraction of a second — but imagine the consequences if all of the action occurred instantly, with no delay at all (such as during reconstruction). That would cause much more damage. It might shatter the arm, rupture blood vessels and tear flesh that would otherwise have been only bruised.
I therefore suggest that this has nothing to do with the transport phase of your teleporter's action. Frankly, whomever engineered the teleporter did a lousy job if they didn't compensate for effects during transport. Have you ever driven in a car that had no shock absorbers or springs? You're going 3-5 miles an hour and it's a back-breaking experience. Now let's take away the cushion (and springs) on the seat and the rubber (and air) of the tires. You can see my point. Engineers long after the invention of such a terrible carriage would never let a potentially harmful condition arise. And if they were tempted to due to corporate greed or something like that, no decent bureaucracy would ever allow it lest the users of said transporter start voting for someone who will fix the problem.
Reconstruction is your enemy
Which means we're talking about something during the reconstruction phase of the experience that's leaving people feeling like they've been turned a bit inside out. In other words, there's no actual danger in the teleportation experience. It's perfectly safe by design. But there's no way to stop you from feeling weird about it any more than a safe boat trip on a calm, sunny day can still leave you utterly sea sick.
Said better: all of the conditions you mention in your post like "spatial warping" is nothing more than the technobabble that rationalizes the idea of "and that's all compensated for during reconstruction" which is what results in the feeling of sea sickness.
An example: I remember reading a short story once about a space traveler having to make a choice to use an emergency teleporter due to system failure. He was sure to die if he didn't use it. What was the crux of the story? In that world, teleporters didn't move the unique person from one place to another. They were more "realistic" in that they were duplicators. Once you pushed the proverbial button, what appeared on the planet was a duplicate of yourself. One that was perfectly safe.
But "you," the original "you," were still on the ship... dying in a very horrible way.
If I recall, the story investigated themes like what it was like to use a life-saving device that still made you feel complicit in a horrific death. What it meant to realize that you were not really you — that the flesh had never been touched by a loving spouse or had even touched the fabric of clothing before, but still had the memories of those things. If I recall correctly, the story even touched on the philosophical question of, "am I really me?"
So I recommend you change your focus a bit
If we ask the question, "what could make me feel the equivalent of sea sickness in an energy teleporter world?" you have everything from "am I really me?" types of psychoses to the "vibration" of the atoms in your body not being quite the original, which would still let you live just fine, but could rationalize feeling really weird.
But to give you a better or more focused idea of what could specifically cause these feelings in your world would require a much more specific explanation of how the teleporter procedurally operates. From the moment someone decides to use the machine to the moment they walk away after transport, what is happening to them step-by-step?
E.G., my machine solves the duplication problem by destroying the original body. It's actually part of the process. It's impossible to "interpret" or "read" the structure of the body and its energy without dismantling it in the process. This means that some part of the brain is "feeling" this experience of "dying" the instant before dematerialization is complete and that feeling is retained... ah-hah!
But as you think about that, remember that the result of the teleport cannot have in any significant or measurable way any actual change to the physical body — otherwise you have everything from a vegetable on the transporter pad (synaptic pattern failed to resolve, nobody's home anymore) to a pile of mush.
