This paper provides a perspective on the literature and current challenges in Multi-Agent Systems for interoperable robot navigation in industry. The focus is on the multi-agent decision stack for Autonomous Mobile Robots operating in mixed environments with humans, manually driven vehicles, and legacy Automated Guided Vehicles. We provide typical characteristics of such Multi-Agent Systems observed today and how these are expected to change on the short term due to the new standard VDA5050 and the interoperability framework OpenRMF. We present recent changes in fleet management standards and the role of open middleware frameworks like ROS2 reaching industrial-grade quality. Approaches to increase the robustness and performance of multi-robot navigation systems for transportation are discussed, and research opportunities are derived.