The essence of our global society's learning environments is facing significant changes due to digitalization. This process prompts an accelerated integration of industrial and academic approaches and practices to cope with contemporary challenges. Universities and companies can benefit from recent progress in developing tools that allow real and virtual worlds to converge into Cyber-physical systems (CPS), mainly because such systems can be engineered for instructional and technological purposes. This chapter describes the design and rationale behind developing a thought-provoking learning factory experience that employs CPS to connect the manufacturing and pedagogical perspectives with a machine motion control task. We address the development and validation of an on-the-fly box labeling machine as an illustrative case, integrating a physical controller, a set of industrial servo motors, and a machine's digital twin. This system aims to provide academic challenges in a flexible manufacturing environment, where engineering students are exposed to professional experiences such as teamwork, formal communication interaction, and problem-solving competencies. The functional machine design and validation follow a top-down mechatronics approach. The integration of mechanical, electrical, and automation aspects in the CPS is conducted through physical devices, simulation technology, and real-world tests. The results show the approach's feasibility and restrictions, providing a bridge between the industry and the academy to promote machine automation's disruptive education.