Recent technological advances encompassed by the smart factory concept have fundamentally changed industrial control systems in the way they are structured and how they operate. Majority of these changes affect Supervisory Control And Data Acquisition (SCADA) systems, shifting them to a higher level of interoperability, heterogeneous networks, big data and toward internet technologies and services in general. However, this transformation does not affect all SCADA systems equally. The immediate industrial environment and controlled processes have a significant impact as well. This paper presents a holistic approach to SCADA systems implemented in continuous flow production control within the steel industry production environment. We outline the multi-layer architecture of the SCADA control framework and the aspects of interoperability and interconnection within the architecture reference models, together with the research challenges and opportunities arising from the recent rapid increasement of the industrial control systems complexity and digital transformation under the Industry 4.0 paradigm, resulting in disrupting levels of the traditional automation pyramid based on Purdue model toward a higher level of integration and interoperability enabling cross-level data exchange empowered by the Industrial Internet of Things. Furthermore, the paper addresses the problem of proprietary SCADA systems and elaborates the causal correlation between SCADA quality requirements and adoption of new technology in relation to the specific industrial environment of the steel manufacturing process.