Control system optimization has long been a fundamental challenge in robotics. While recent advancements have led to the development of control algorithms that leverage learning-based approaches, such as SafeOpt, to optimize single feedback controllers, scaling these methods to high-dimensional complex systems with multiple controllers remains an open problem. In this paper, we propose a novel learning-based control optimization method, which enhances the additive Gaussian process-based Safe Bayesian Optimization algorithm to efficiently tackle high-dimensional problems through kernel selection. We use PID controller optimization in drones as a representative example and test the method on Safe Control Gym, a benchmark designed for evaluating safe control techniques. We show that the proposed method provides a more efficient and optimal solution for high-dimensional control optimization problems, demonstrating significant improvements over existing techniques.