This paper proposes a scalable Bayesian optimization (BO) framework for dense base-station (BS) configuration design. BO can find an optimal BS configuration by iterating parameter search, channel simulation, and probabilistic modeling of the objective function. However, its performance is severely affected by the curse of dimensionality, thereby reducing its scalability. To overcome this limitation, the proposed method sequentially optimizes per-BS parameters based on block coordinate descent while fixing the remaining BS configurations, thereby reducing the effective dimensionality of each optimization step. Numerical results demonstrate that the proposed approach significantly outperforms naive optimization in dense deployment scenarios.