I added JBullet support to Releases of BowlerStudio 0.8.0+. This means your kinematics, walking, simulation scripts can all take into account physics as part of your control schema. This will also allow me (or some ambitious contributor) to add a full simulation environment for creatures. This will let you test walking gaits to see if they will work in the real world of physics.
This project is starting to feel more and more like a game engine targeted towards designing robotics and engineering tools.