What I hope is a helpful suggestion to make altering the food options for each dragon easier than altering a new world every time. I'll understand if there's an essential tactic I've just missed.

There is a folder called "defaultconfigs" in any folder in mc. Just add your serverconfig there and you won't have to change the settings every time.
But we still recommend deleting all configs before major updates. It's much better if you just manually copy the list into a new generated config.
We don't want to forcibly remove configs. Although the idea often comes up because of common complaints about people not following the recommendation to remove configs.