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I'm just putting this here for future reference in case anyone is confused by why this is an issue or needs a reminder of the issue. As Jim says this is explained in the tech note above.
Fundamentally the sky model comes from a model from ESO which is measured light coming from the sky including airglow etc. So the light is leaving the atmosphere and going into the pupil. Therefore it doesn't make sense to include the extinction going through the atmosphere.
There's a thread in slack where Lynne Jones mentions this and references SMTN-002, particularly footnote 1.
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