TheZero Since you seem to be going down a rather difficult path, I would like to confirm your reasons for doing this. Is it not possible to achieve what you (or your customer) want to do by repacking the textures after attaching sprites that are not included in the texture atlas, as demonstrated in Spine Examples/Other Examples/Mix and Match Equip
?
Or, since you mentioned "taking an element from the atlas and manipulating it", if you need to change the material of a specific slot, you can use SkeletonRenderer.CustomSlotMaterials
as described in the Changing Materials Per Instance section in the documentation. Would this not help for what you want to do?