This is only my personal take, but I think that Phoenix didn't amped her psychic abilities, but accelerated her potential. In the past, when Jean had not discovered the full reachness of her power, some of the psychic feats she demonstrated as Phoenix may seem like things she could only do with the amp of Phoenix. But later, those things were done by Jean alone. For example, when she rearranged the particles of her clothes in the DP Saga, Scott was surprised because Jean had never done that before. In the Morrison run we learn that Jean was already perfecting herself in the art of the molecular telekinesis. In Percy's X-Force, she used her molecular TK to disintegrate the plant-people of Tierra Verde. In New Mexico, Jean-Phoenix uses her power to keep Scott's eyebeams "off" so he can look at her. Jean did the same thing without the Phoenix help in the Rosenberg run.
One can say that Phoenix helped her to reach a higher level faster.