Yes, the constantly changing flow is far better for the system.
Another way to acomplish a varied flow within the tank is the use of flow deflectors. Hydor makes a rotating deflector, powered by the waterflow, that easily mounts to the output of many powerheads. There are a few downfalls to the use of these. They are a bulky addition to the powerhead, and are not aesthetically pleasing. They occasionally freeze up and need regular cleaning, and will occasionally blow off of the powerhead.
Another method, albeit far less effective, is to direct the flow of two powerheads directly into one another.