This study is the first to investigate LLM comprehension capabilities over long-context (LC), clinically relevant medical Question Answering (QA) beyond MCQA. Our comprehensive approach considers a range of settings based on content inclusion of varying size and relevance, LLM models of different capabilities and a variety of datasets across task formulations. We reveal insights on model size effects and their limitations, underlying memorization issues and the benefits of reasoning models, while demonstrating the value and challenges of leveraging the full long patient's context. Importantly, we examine the effect of Retrieval Augmented Generation (RAG) on medical LC comprehension, showcasing best settings in single versus multi-document QA datasets. We shed light into some of the evaluation aspects using a multi-faceted approach uncovering common metric challenges. Our quantitative analysis reveals challenging cases where RAG excels while still showing limitations in cases requiring temporal reasoning.