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Solved the Problem, it has nothing to do with the urdf. MoveIt just does not recognize our kinematic chain correctly.
Our kin. chain should look like the following: r_arm: base_link -> r_tool0
So what I did was:
Problem is getPlanningFrame() always returns "world" frame. So our custom IK system uses "base_link" as reference frame, while MoveIt uses "world". I discovered a lot of people experiencing this bug and there seems to be no solution, we will transform everything with tf2 now.