High profile systemic safety standards for Cyber-Physical Systems (CPS) development within the transportation domain have commonalities with regard to their view of the safety-related implications of tool usage. Their guidelines on tool qualification favor a bottom-up approach in which tools are dealt with in isolation and mostly if they may directly introduce faults into end products. This guidance may ignore risk introduced by the integration of software tools, especially if these risks are related to low levels of automation - such as process notifications and improper graphical user interfaces. This paper presents a study that ties weaknesses in support environments to software faults. Based on the observed weaknesses guidelines for a top-down software tool chain qualification are suggested for inclusion in the next generation of safety standards. This has implications not only for the surveyed standards in the transportation domain, but also for other standards for safety-critical CPS development that do not include a broader view on risks related to tool usage. Furthermore, given the type of omission identified in the surveyed standards, it is suggested that researchers interested in the safety-related implications of tool integration should approach organizational research in search of possibilities to set up theory triangulation studies.