There are proprietary pedestal systems that provide a very stable, level and serviceable deck over a roof membrane, though they are relatively expensive compared to conventional methods.
In whatever manner a deck is constructed over a roof, maintenance for cleaning and repairs of the membrane below is recommended. Deck “panels” should be constructed that can be lifted with minimal effort or damage. The roof below should be cleaned and inspected at whatever intervals is found necessary for each deck. A deck located under pine trees will need much more maintenance to clean out debris than a rooftop deck above a high-rise.