Discrepancy between MATLAB and Simulink closed loop response?
I would say you are doing something wrong in using matlab

num_plant = [0.0001 10];
den_plant = [0.005 5 0.6616 61.01 2.11 20];
G1 = tf(num_plant, den_plant)

num_controller = [46615 6526 5.722e05 2.389e04 2.001e05]
den_controller = [1 404 41605 162000 200000]

C2 = tf(num_controller, den_controller)
G2=G1*C2; %G1 is same 5th order TF as Simulink
new2 = feedback(G2, 1);
step(new2,50)
grid


This produces:


And in simulink



All intent and purposes... identical.



In fact executing: [y,t] = step(new2,50) and playing back in Simulink shows this