>>350622241
It's situation dependent. 
If a mesh is typically off and is rarely enabled, then a game object toggle is the best for performance.
A shapekey toggle will be overall slightly more expensive since you're always rendering the object, but I'm not sure if it's more expensive than just having extra renderers/ meshes for each toggle you want. 
Silent's wizardry I'm not sure about. From the little I've heard it's at least better than a shapekey toggle, but won't work if someone has blocked your shaders. I'm also not sure if there's much overhead for the system itself.
Material swap to transparent should be your last resort. You're adding another draw call that is always enabled that other methods or blender work can typically fix.

Also I wouldn't take the avatar perf rank as gospel, especially with 3.0: Someone with two meshes (one skinned renderer for the face, one normal for everything else) but is 70001 tris will be very poor but still be significantly better performance than many medium rank avatars. 

For manual atlasing I used Kattsune's guide to manual atlasing for 2.8, which gave me enough to get started with baking in 2.8.