We have an example scene on our roadmap which shall demonstrates the usage of lots of equipable items in large atlases. We will let you know as soon as this example scene is done and included in the Spine Unity Runtime.
For now we can only recommend you to create the atlases based on draw-order, as Nate descibed above:
If you want to avoid this then it is most efficient to use a single texture. If you can't do that, then you can use subfolders to control which images are packed to the same atlas page. Arrange your images based on the most common draw orders for your skeletons to minimize texture switches. For example, the first half the attachments (based on draw order) on one atlas page and the rest on the other.
If you create one atlas with your character's parts that are in the back (e.g. the character's half-naked parts with underwear on) and one or more atlases with parts in the fromt such as equipable items (e.g. armour, boots, gloves, etc), then your setup should be good in terms of drawcalls, as it does not need to switch atlases too often.
What would be bad atlas grouping is the one that you encountered above, by having parts from back to front draw order in different atlases all the time.
So as an example, when we have a caracter with front items [f1]-[f3] and back items [b1]-[b3] viewed from a camera:
camera
[f1][f2][f3] [b1][b2][b3]
This would be good atlas grouping:
- BackAtlas with image items
[b1][b2][b3]
- FrontAtlas with image items [f1][f2][f3]
This would be bad atlas grouping:
- MixedAtlas1 with image items [b1]
[b3]
[f2]
- MixedAtlas2 with image items
[b2]
[f1]
[f3]