Thanks @trusktr for your response.
I was looking into the Flamingo example on Three.js website that looks like it might work for me.
https://threejs.org/examples/?q=gpgpu#webgl_gpgpu_birds_gltf
Using the Flamingo model as reference, I could strip away the armature from my skinned model and convert the Bone animations into Shape Key animations. This way I could export a clean mesh with one flying animation and vertex colors (just like the Flamingo model).
I have already optimized the flock calculations on the CPU using octree. I was wondering if I could use InstancedMesh to render all the geometry and also play the animation on that mesh. Does that seem possible? I guess that loops back to your original question, but now the Mesh isn’t really skinned anymore.