Most of this is going to be "eh, agree to disagree" because we just don't have enough data. But I do want to call out a couple of things:

No, both heat up. The air cushion transfers its heat to the object next to it.

Over time, yes. But the bore cap doesn't have very much of it. Heat transfer is not instantaneous; would it be long enough for the air to transfer its heat to the object, before the object reaches the Karman Line? Radiation is pretty quick (like, speed-of-light quick), but conduction is much slower; particularly when one of the bodies (the air) is an insulator. And with iron being an excellent conductor, any heat transferred will be spread throughout the body more quickly than it can be absorbed.

If it disintegrated in the lower atmosphere it wouldn't matter that the air got thinner in the upper atmosphere.

True, but it's not like there's a line (er, well, I mean, not a physical demarcation...there is the Karman Line, but...ah, you know what I mean). Atmospheric density is a decreasing gradient from the ground to the Karman Line. So as it approaches its mechanical and physical limits, the amount of energy acting upon it decreases millisecond by millisecond. Is that enough to save it? Shrug. Not enough data. But it's possible.

Is a metre the original size, or the final size? [of the meteorite chunk]

Actually it's almost three meters, and as far as we can guess that was about its original size. Though in fairness, it was entering the atmosphere at a steeper angle and may even have come down entirely in "dark flight." Still, there are other large meteorites which have impacted at a size greater than 1 meter across, though obviously we have no way to confirm exactly how big they were before they landed.

Rather than getting slowed down initially by the thin upper atmosphere and then only hitting the thick atmosphere once they're slower, they start out in the thickest atmosphere. [...] Something in a thicker medium is going to experience more stress. Try pushing a cracker through the air vs. through water vs. through gelatin. Which medium will cause the cracker to crack first? Obviously it's the thicker medium.

True! But remember, the "reverse meteor" (great phrase, btw) is not hitting the stationary atmosphere at full speed like a regular meteor (or space capsule) does. The iron plug accelerated (incredibly quickly, but it did accelerate) while already in contact with the air above it. This means that the air accelerated at the same rate the iron did, reducing the fracture forces that would seek to crack it. Imagine the difference between swishing your hand in a swimming pool vs. slapping the surface of a swimming pool; it may require more force, but it won't hurt as badly.

OTOH, a meteor is a random collection of rock and metal formed by gravity in space. A pure metal plug cast on Earth is probably going to be a lot less prone to breaking apart.

Oh, great point, and one I hadn't thought about. Something that's an aggregate of 80% iron and 20% "other stuff" isn't going to have nearly as much tensile strength as a homogeneous plate of iron.