Ugh? Of course hardware calibration fixe this issue, why would it not? Theres nothing wrong with the panel
This is just a misuse of terms that is confusing you. You aren't calibrating the display hardware directly. When people say "hardware calibration" on here, they often mean that the output values used to write the profile are measured by a physical hardware device. It's still manipulating how the gpu sees the display and compensating from there. The stock profile doesn't output linear values. If it did and you still saw the black crush, it's unlikely that you'd be able to solve it. Apple seems to use really high gamma value targets on some channels. That might be part of it. I would emphasize that you are very dependent on how they set things at the factory, as they would have the ability to address hardware settings directly.
If I remember right the late 2012 iMac is individually calibrated at the factory. I think this is pretty silly as everything I have read has suggested it is best to calibrate the monitor to your work environment.
Well you could go pretty far with this, but generally what they mean is that the display brightness and color temperature should look similar to the white from your printer under the same light. That isn't the most exact method of doing this, but it's often close enough. Typically I'd start with sRGB, Adobe RGB, or native target settings in the calibration stage, see how it matches, and tweak it from there. Given that you're doing everything from the profiling stage, you really don't want to tweak it further than necessary. I could input 4000K as a white point target, but the results would likely look like crap.
The below information is found on Apple's website.
Vivid, true-to-life color. Every time.
Everything you see on the big, glossy display — from skin tones and dark shadows to bright blue skies and green fields — is rich and vibrant. And the colors are more true to life, too. That’s because every iMac display is individually color-calibrated using state-of-the-art spectroradiometers to match color standards recognized around the world.
This is somewhat ambiguous as there isn't just one standard, and the gamut does not encompass an infinite volume. I would point out that this could be recognized as hardware calibration. They're calibrating hardware. When you plug in that X-rite device, you're just writing a profile to replace that "colorlcd" one with something specific to your display to best match the specified target values at that specific point in the display's life. Further they're measured in the center, so you are still held hostage by the color and luminance uniformity and other things. I want to see more of the newest ones up close.