I believe adding extra risers to a step increases the workload during step-oriented cardio work primarily because the step-up recruits more of the thigh and hip muscles (quads, hams and glutes), plus you're working against more gravity because you're stepping up higher.
As long as your form is good, you can execute the bigger and/or more complex moves safely, AND as long as your knees don't bend more sharply than approximately a 90-degree angle on the step-up, adding height to the step can be a very effective way of increasing your effort. Make sure to plant the foot down through the heel on each step-up, rather than staying on the toes.
A-jock