To achieve a customizable character system in Spine with three different body types (small, medium, large) and various interchangeable parts (pants, torso, head), you can follow these best practices:

1. Single Skeleton with Skins: Use a single skeleton for each body type and create skins for each customizable part. This allows you to reuse animations across different appearances. For example, you can have a "small" skeleton with skins for different pants, torsos, and heads.

2. Skin Bones and Constraints: Utilize skin bones and constraints to handle different proportions and unique animations for specific body parts. This ensures that only the relevant bones and constraints are active for the selected skin, optimizing performance.

3. Runtime Repacking: Instead of loading all images at once, use runtime repacking to load only the images needed for the selected skin. This can significantly reduce memory usage and improve performance. Refer to the Runtime Repacking section of the spine-unity documentation for more details.

4. Mix and Match: Implement a mix-and-match system where you can combine different skins programmatically. This allows you to create a variety of appearances without cluttering the project with numerous predefined skins. Check out the spine-unity Mix and Match documentation for guidance.

5. Organize Skins by Theme: Group skins by theme or style to keep the project organized. For example, you can have a set of skins for "casual" outfits, "armor" outfits, etc. This makes it easier to manage and load the necessary assets.

6. Optimize Performance: Test the performance on target devices and apply common optimization techniques such as reducing the number of bones, using point bones, and minimizing the number of active attachments. Refer to the Spine User Guide on performance for more tips.

By following these practices, you can create a flexible and efficient system for customizable characters in your game.

Yimec As Spinebot has already recommended, characters with different proportions can be realized with the same skeleton by using skin-constraints. You may find our blog post below helpful:
https://esotericsoftware.com/blog/Skin-constraints-for-different-proportions

This gets really complicated very quickly.

How would you handle modders adding new parts? Let's say we ship with 3 heads and a modder adds 3 more?

In my case, I'm not working with Unity. Repacking doesn't seem to be a thing in spine-c.

rr-reinhart How would you handle modders adding new parts? Let's say we ship with 3 heads and a modder adds 3 more?

On what level does a modder add 3 more heads? Does he have the Spine project available? If not, how does he specify the size, name, etc of a head attachment? Or will you just support Texture-replacement with requirements of being of equal size like the original, and provide templates for each body part or attachment?