Yes, the boost will be smoother with the wastegate always open and bleeding air around the turbine wheel, vs the boost controller opening and closing the wastegate door that will cause some minor boost wave. Controlled boost is never perfectly smooth with a correctly set up internal wastegate. Your set up is spooling much slower because of this than if the pre-load was set correctly. Is it hurting anything? It is making difficult to control boost at higher loads because the duty cycle is being required to be set higher than normal to get 15 PSI. When we do not build the car and only tune it with limited time on a tuning trip, we do our best to dial in the car the way it set up. If I had the car at my shop we would have readjusted the wastegates. If you want the full powerband your set up can offer, you need to tighten your wastegates. It has nothing to do with longevity or keeping the boost lower. If you set up the wastegate pre-load properly, you will be able to run lower boost controller duty cycle and this will keep the boost from creeping at higher loads and will only make a power band larger and add more safety.
