I am using Unity 2020.2 alpha, and not sure if this applies to the other versions of Unity, but here is what I have found :
When you have custom secondary texture such as say _EmissionMap, it all seems to work until when you are adding sprites to the atlas v2 using folder.
Using Folder and adding them to the Atlas is a great way to save time and reduce man made mistakes. But when you add custom secondary map at the same folder as the sprite, it also packs that. This does not happen for the normal map because Unity recognizes it somehow and exclude them from packing with the normal sprite sheet.
We would like to have option to have this happening with our other custom secondary maps so that we can neatly organize them within the same folder with file names such as
sprite
sprite_n
sprite_e
…
instead of having to manually add them one by one or have to have separate folders. Unity, please make this happen! It will benefit everyone.