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
exactlymore or less the same speed and furthermore, are not accelerated in any way, except for the atoms that the ship pushes out of the wayI'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.