Why simulink step response differs from matlab's step function?
This is a numeric issue caused by the simulation step size. The system poles have real parts in -0.4e6, and as can be seen in the matlab 'step()' result, the settling time is lower than 2e-5.

Using simulink default simulation parameters, the system response will be evaluated in time-steps that are larger than what is necessary to describe what is really going on, similar to a Nyquist sampling criteria.

To get correct simulation results with your system, I've done the following:


Open the 'Model Configuration Parameters' (cog icon);
Change 'Stop Time' to 2e-5;
In 'Solver Options', change 'Type' to 'Fixed-step' and 'Solver' to 'ode8 (Dormand-Prince)';
In 'Additional options', change 'Fixed-step size (fundamental sample time)' to 1e-7.


Now the simulation runs as expected. Proof: