An apparatus includes a body and a shaft assembly. The body includes a rotary drive output, a linear drive output, and a control module. The shaft assembly includes a distal end and a proximal end. The distal end includes a type of end effector configured to operate on tissue. The proximal end is configured to removably couple with the body assembly. The proximal end includes one or both of a rotary drive input configured to couple with the rotary drive output or a linear drive input configured to couple with the linear drive input. The shaft assembly is configured to actuate the end effector in response to movement of one or both of the rotary drive input or the linear drive input. The control module is configured to selectively actuate the rotary drive output or the linear drive output based on the type of end effector of the shaft assembly.