I am new to this community so I'm not able to respond to other answers. You specifically mention that the FTL drive works by using an "<PERSON>-style warp bubble" and people seem to not be knowledgeable on what that entails and apparently unwilling to spend a few seconds on google to find out.
This drive works by expanding space behind the craft and shrinking space in front of the craft to propel it forward, propelling the craft at FTL speeds. This is almost a perfect analogy to how atmospheric pressure differences cause liquid to rise up a straw, propelling liquid into your mouth.
The craft, if moving at all, would only be using it's main engines enough to thrust into the next zone of shrunken space, it would actually be traveling at a rather low speed, enabling it stop almost on a dime, as it were. This is one of the methods theorists believe "observed" "alien" craft travel, allowing them to make immediate turns, and velocity changes without any delay. The G-forces of some of these "observed" craft would be enough to kill a human outright.
This rules out air resistance. The craft is barely moving, it at all.
This engine also does not work using <PERSON>'s third law of motion, as it is not an exhaustive engine; Modern rocket engines work by pushing particles out of the bottom, this does not. Thus, this also rules out saying things like "By engaging your warp drive, you just detonated 500 billion trillion nuclear bombs on the surface of Earth". Although you do require that much energy to achieve your result, the energy is not expelled from your craft.
From my perspective you really only have 2 options here
* The space distortion is so large that it engulfs the planet you are in because of science reasons. Expanding or contracting the space that a living create exists in probably kills it. It also would destroy the planet itself probably. I'm no physicist, but probably.
* The second and probably one you'd want to go with since this builds off of an idea that you came up with yourself, negative matter. 947
You could again go 2 different ways with this.
+ Negative matter is a colloquial equivalent of antimatter. Creating a ton of negative matter in atmosphere is a pretty good way of ensuring that a ton of it interacts with the atmosphere. Congratulations, by firing your warp drive you have just detonated 500 billion trillion nuclear bombs on the surface of Earth, killing yourself and the entire planet.
+ Negative matter is not a colloquial equivalent of antimatter, but more like the mathematical concept of negative. Using the very simple equation 1 + (-1) = 0, every bit of negative matter you create collides with the atmosphere and blinks out of existence and your drive fails to function.
Edit in response to <PERSON> edit
I still don't really agree with the conclusions you've drawn. I used an analogy about sucking liquid through a straw, but with more thought I think a better analogy is surfing. The alcubierre drive creates a "wave" so to speak and the ship simply rides it. Less abstract, if you shrunk the space in front of you from 100 meters to 1 meter, by moving 1 meter and expanding space behind you back to it's normal "width", you've actually moved 100 meters.
* Regarding air molecules, that is not what would happen. The drive only compresses or expands space itself, it does not directly interfere or interact with the atoms and molecules within. However, a possible consequence of this that I didn't think about before is that compressing space with atmosphere in it would create a very real "wall" of air, which actually exponentially brings air resistance back into this equation and the challenges that presents. The ship could burn up and be destroyed before actually escaping the atmosphere
* Atmosphere is entering and exiting the warp horizon at exactly more or less the same speed and furthermore, are not accelerated in any way, except for the atoms that the ship pushes out of the way
* I'm not sure why a cylinder of atmosphere would be removed, I assume that's due to the conclusion that the inside of the warp would collect atmosphere faster than it can exit as it travels but that wouldn't happen
* "gravitational and electromagnetic interactions between matter and energy inside the warp bubble and matter and energy outside the warp bubble" You may be onto something here as being inside a gravity well strong enough, such as a planet, could introduce variations in the "compression-ratio" significant enough to rip the ship apart when the drive engages. Even if that wouldn't happen, I think it definitely sounds SCIENCEY! enough to be plausible.
Further regarding compressing matter, Film Theory did a video on Ant-Man before and he said that compressing a human to the size of an ant would cause the molecules to get so close together that you would collapse into the singularity of a black hole and consume the entire planet. 947