Or can someone explain how I might map a "mask" texture to one that is packed in an atlas? The UVs would not align so my simple shader test for that will no longer work.

Say for example I have greyscale clothing piece in my skeleton. I get access to it via a slot node and want to create a custom shader which reads from a mask, which is just red, green, and blue values in certain spots, to recolour the clothing. So I can say, wherever there is red in the mask should be purple tint in that area on the clothing.

Is there a way to setup the skeleton data resource without a packed atlas, similar to how Spine read the textures from folder(s)?

Busy evaluating whether Spine would fit with my new project and was just about to ask whether SubViewport is our only option to get Spine to render to 3D. I did a quick test with a Sprite3D rendering the viewport and it seemed to work okay but an official Sprite3D-like would be nice.