Automation and robotics are two enablers for developing the Smart Factory of the Future, which is based on intelligent machines and collaboration between robots and humans. Especially in final assembly and its material handling, where traditional automation is challenging to use, collaborative robot (cobot) systems may increase the flexibility needed in future production systems. A major obstacle to deploy a truly collaborative application is to design and implement a safe and efficient interaction between humans and robot systems while maintaining industrial requirements such as cost and productivity. Advanced and intelligent control strategies is the enabler when creating this safe, yet efficient, system, but is often hard to design and build. This paper highlights and discusses the challenges in meeting safety requirements according to current safety standards, starting with the mandatory risk assessment and then applying risk reduction measures, when transforming a typical manual final assembly station into an intelligent collaborative station. An important conclusion is that current safety standards and requirements must be updated and improved and the current collaborative modes defined by the standards community should be extended with a new mode, which in this paper is refereed to the deliberative planning and acting mode.