I'm not a chem expert, but the way I've heard it explained is that all the encap cleaners have some carpet protector in them. This is part of how they work, this helps the encap cleaner keep the soil off the carpet after it's removed until vacuuming. Thus if you use an encap cleaner, it is preferable to use a protector it is designed to work with.
Releasit punch and encap clean both have soileze already in them, so using extra soileze as your protector would be the logical choice. I believe that Whamm and Enc are synergistic with a product called Fiber Cop. I'm not sure about any others.
I don't know if there are any contraindications with all natural cleaners. Maybe the same synergies apply or maybe since you have padded up almost all the cleaner it's ok to use any protector... Not sure on this one, maybe someone else knows.