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This kilometre of air analogy is very misleading.
The 'thickness' is not what matters. The effect is important. It's a bit like putting a piece of paper in front of your scope. Someone might comment that, as the light has travelled billions of km uninterrupted, what is the problem with a little obstruction less than 1mm thick? Well, I think you could tell at the eyepiece what the problem is. Similarly, most of the atmosphere is transparent to IR radiation but that little 38mm of CO2 does make a difference. And the change from pre-industrial 280ppm (28mm) to 380ppm also makes a difference.
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