If you want to export from Spine, you can simply import all the skeletons in a single Spine project, (without having to move each mesh into the same skeleton) then export. You can also choose if you prefer to have an atlas per skeleton or a unique atlas for everything. I think this solution is great as you can just deactivate the skeletons you don't need when working on something so that they won't clutter your view, and you have less files to manage.

If you prefer to have separate Spine projects, another way to automate this is to use the command line to pack textures:

Texture atlas packing:
-i, 

---

input   Path to folder of images to be packed.
-o, 

---

output  Path to write texture atlas and PNG files.
-j, 

---

project Path to a project to determine which images are used by meshes.
-n, 

---

name    Texture atlas name, the prefix for the atlas and PNG files.
-p, 

---

pack    Texture atlas name or path to pack settings JSON file.

Texture Packing - Spine User Guide
Export - Spine User Guide: Command line

It is possible! But only from the command line:

Spine 

---

help
...
Texture atlas packing:
-i, 

---

input   Path to folder of images to be packed.
-o, 

---

output  Path to write texture atlas and PNG files.
-j, 

---

project Path to a project to determine which images are used by meshes.
-n, 

---

name    Texture atlas name, the prefix for the atlas and PNG files.
-p, 

---

pack    Texture atlas name or path to pack settings JSON file.

You can specify -j or `

project` multiple times. For example:

Spine -i /path/to/input/images -j project1.spine -j project2.spine -o /path/to/output -n atlasName -p /path/to/pack.json