Modular automation provides a challenge for traditional physics simulators, especially if they are used as a simulator in the loop of a development or research project looking at behavior from a systems level. In this paper, we present extensions of a previously developed simulation environment that is tailored to provide these characteristics. The extensions include simulation engine level improvements, such as including better modeling of the material flow, and sensor anomaly injections to model sensor faults or tampering, as well as system-level enhancements and functionality including certificate handling and anomaly detection methods using machine learning. This simulation environment has proven useful for education as well as research and engineering work, and with the provided extensions several new directions of use can be envisioned. The system is demonstrated in the use case of a modular ice-cream factory, including all the new and enhanced functionalities.