You need a longer rear shock. 4600 is stock length.
The thing that limits the rebound of the rear suspension, is the shock. Raising it with a puck under the spring, just trades rebound for jounce.
Correct me if I'm wrong, the thing is, the 5100/4600 are the same thing for the rear, its just that the 5100 is longer. You raised the rear suspension, so the suspension needs to go lower to get the same wheel travel, so if you use the 4600, which will work, but you've decreased the suspension ability from stock, going with the 5100 you've increased the suspension ability.
If you're just doing it for looks and won't be doing any off roading serious enough to hit the limits of suspension travel, its likely NOT going to make a difference.
The front suspension is different, the same thing doesn't apply. Since the front 5100 has a adjustable spring perch that at its lowest setting is 3/4"-1" higher than stock, combined with the lift block will make the front higher than you would want, so you need to use the 4600 to avoid that.
Someone more familiar with Lifts would have to chime in, I'm NOT sure what limits the rebound of the front suspension, so a longer shock might NOT be any advantage for a lift in the front of the Commander. Regardless, the 5100 itself will increase the front lift and with a lift kit, it will now go from being rear high to front high and NOT level.
Like stated before the 5100 and 4600 are the same performance, so mixing them front/rear should NOT be a problem.