To your questions:
- NO. rigidBodyTree in Robotics System Toolbox is designed to be stateless. So there are no joint positions/velocities/accelerations on the robot objects. These quntities are passed in as input argumetments to robot methods, such as getTransform, or inverseDynamics.
- NO. the geometricJacobian is just a matrix that relates joint velocities to end-effector velocity. It is also conifguration-dependent, so it's typically written as J(q). To get the end-effector velocity in Cartesian space, you need to provide your vector of joint velocity qDot, and do xDot = J(q) * qDot;