Can I remove my step response overshoot?
In a series controlled motor arm, the mechanical inertia and hysteresis and high slew rates, it is normal to have overshoot. Damping the input with a LPF blocks the spectrum that results in the overshoot but also reduces phase margin in the feedback loop. Putting the LPF after the loop may be impractical with a shock absorber to the arm or loading the output mechanically both reduce the overshoot.
Reducing the Kp gain  will reduce the slew rate and thus the spectral content that produced the overshoot,BW -3 dB = 0.35/Tr (10 to 90%) but also reduce the phase margin in the loop.
In human arms and legs all muscles are bipolar opposing forces that contract and relax to control force and position.  If you can modelled your design on this , then the hysteresis would drop and stability would be far better with opposing motors keeping the minimum tension for control, stability and rigidity from interference.
The problem logically is the stored energy to accelerate is not scaled to the load which might vary so the step response will change unless you change your maximum acceleration/torque current and use a profile that ramps up then predicts when to deaccelerate with zero overshoot in the fastest possible time.  This is how arms work in magnetic hard disk drives (HDD). So there are 3 controls for a,v,x with multiple feedbacks for current, servo velocity and position error.  This is how I think you ought to control your system, not by analyzing the step response. Keep in mind thermal effects on motor torque and load variations that dampen the response as well as hysteresis.