I'm automatically launching node-red via systemd, I'm not hot to dive into how it is actually doing it, so changing the command line would be a last resort.
The second method suggests I wouldn't have the problem if the default flows file was flows.json instead of flows_hostname.json.
On the next system I clone, I'll edit settings.js and un-comment flowFile to make it:
Presumably when the cloned system boots with the new hostname it'll then still use the original flows file.
Short answer, no, haven't tried it yet, but I will be cloning another system (AtomicPi) in a week or two. I'll follow up if it doesn't work.