Hi there Erikari,
I can't send you the scene file because I'm working under an NDA, unfortunately.
However, the problem is definitely not in the settings. I am able to export the same scene perfectly fine with those exact settings in 3.7.93 (which I've reverted to), but NOT in 3.8.11.
Oh, also I can tell you that the images in my scene are sourced from a single PSD, and its dimensions are 768x1874 pixels, and there is very little overlap in the images (some extra hand variations and some overlap at joints) . So there is simply no way that the atlas would end up being over 2048x2048 pixels unless there is a packing error. 4 px per edge certainly would not make a difference 🙂