What the radiation thermometer reads, looking at the background of outer
space, overlaid with a transparent but blackbody-radiating layer of
atmosphere...

Which absorbs IR...

No, like all matter, the atmosphere both emits and absorbs radiation. At
night it emits more than it absorbs (thus cooling itself while keeping us
warm down here, happily), so it is a net emitter, not an absorber. When
you point your Raytek at the clear night sky, you are measuring that
emission. If the atmosphere (net) absorbed IR, the sky would feel
cryogenic like outer space, instead of just somewhat cooler than the
surface, on a warm, clear night.

There is this mythology of the atmosphere (glass, etc.) being nothing but a
sink for radiation. Just enough physics to get it wrong. Typical of
global warming advocates.