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Since I can't take a good photograph of it, here is a mockup I made in Photoshop that simulates exactly what I saw (I had compared them side by side, it is really perfect):
The issue lies in the integrated LCD. Sharp edges are rendered in a fuzzy way. It seems that every pixel is blended very lightly with its four adjacent neighbors. This becomes instantly noticeable with non-antialiased text, or pixel art (which I work with primarily). It would seem that the Intel HD 3000 is applying its over-aggressively-tolerant anti-aliasing algorithm on native resolution images, which it normally reserves for scaled resolutions. I doubt this is the drivers' fault, as this problem does not manifest on an external monitor, screenshots, or other laptops with HD3000 graphics I have used. I am fairly certain that scaling operations on the internal panel are not done using the GPU directly, but rather done by the minor hardware responsible for driving the LCD from the Intel GPU's output. That is why I feel this problem may be localised to just the X220 or other similarly configured computers.
I am mostly curious if this happens on any other ThinkPads, notably the non-IPS X220 or the new X230.
I was trying to find out on Intel forum whether the 9.x driver version contains such permanent anti-aliasing feature that got activated but it is impossible to get an answer these days. If I only could talk directly to the driver developers I am sure the issue will be resolved soon.