Fairness research in machine learning often centers on ensuring equitable performance of individual models. However, real-world recommendation systems are built on multiple models and even multiple stages, from candidate retrieval to scoring and serving, which raises challenges for responsible development and deployment. This system-level view, as highlighted by regulations like the EU AI Act, necessitates moving beyond auditing individual models as independent entities. We propose a holistic framework for modeling system-level fairness, focusing on the end-utility delivered to diverse user groups, and consider interactions between components such as retrieval and scoring models. We provide formal insights on the limitations of focusing solely on model-level fairness and highlight the need for alternative tools that account for heterogeneity in user preferences. To mitigate system-level disparities, we adapt closed-box optimization tools (e.g., BayesOpt) to jointly optimize utility and equity. We empirically demonstrate the effectiveness of our proposed framework on synthetic and real datasets, underscoring the need for a system-level framework.