VNAV
Thanks for the feedback.
It seems that procedures are very much operator specific, plus dependent on the aircraft performance and interval between the various crossing altitudes of the step climb.
In the example of CPT5X, I had setup and briefed as described with the final altitude selected in the MCP. On handover from tower to departure we were instructed to "Stop climb A3000" and then reprimanded for having A5000 selected, and advised in future to select the first step altitude.
I think VNAV is a valuable tool in the right circumstances but it caused conflict in terms of the wider system, which was something I hadn't anticipated. At the end of the day, fitting seamlessly into the system is the goal!