Though the outputs do not match, this is not a bug. The Control System Designer seems to act differently because it computes the response assuming a specific controller architecture. This architecture can be edited in the "Edit Architecture" dropdown menu in the toolstrip of the Control System Designer. By default, the controller architecture is a closed loop system as shown in the image below:
Thus, the step response plotted in Control System Designer is the response of the system with the feedback loop as shown in the image above.
To get open loop response for the transfer function, please follow the steps listed below:
1) The step response plot is for “IOTransfer_r2y”. Find the label "IOTransfer_r2y" in the "Responses" list on the bottom left of the Control System Designer window and double-click on it. The screenshot below shows where the label "IOTransfer_r2y" is located:
2) Double-clicking on the label will open up another window. In this window, open the loop “ym” by adding it to “Compute input/output response with the following loops open” list as shown in the screenshot below:
3) Then click "OK". This closes the window.
Now, the step response in the Control System Designer is updated and it should be identical to the response obtained using the "step" function.