What does "mesh morphing"/deform timeline have to do with physics integration?
You can still manipulate bone world values (the 2x2 world rotate/scale/shear transform matrix and world position) at runtime to integrate with physics. That way you can still leave the rendering to SkeletonRenderer code, and even interpolate between animation-controlled and physics-controlled positions.
If not, you can switch to your own renderer, and render all the attachments, pretending your box2D bodies or whatever analog, are bones (which are really just transforms in a hierarchy).
The first way is probably better.