GTM ZoneRunner with iControl REST, possible?

It is true there is no cli support for ZoneRunner. As you mention the knowledge base article gives you the path to safely update the named files via the command line. Armed with that knowledge, it would be possible to create a tmsh script or iApp to implement that logic and then you could pass data via REST to use with those tools. Not an easy task to get right, but there are indirect options that can be explored. I discuss this as part of this week's Post of the Week video.