In AEM/CQ versions past, as in prior to AEM 6.0 and 6.1, if a publish instance was to go down and time was of the essence, you could always shutdown the author and copy the author repository over top of the publish repository. Once you brought up the publish instance, it would behave like a publish instance and you'd have all the content of the author instance with no need for long and costly activation of basically everything. You could work out the finer details later right?

Those days are long gone. It appears according to this documentation from Adobe and my real world testing the run mode is somehow embedded into the repository at first run of the instance. Subsequently, changing the run mode of the start script, will not change the run mode of the repository and the instance will behave as the instance it was cloned from.

What this means is that even though the jar was passed the publish runmode, the backing datastore is configured as an author, which then will cause the publish instance to behave as if it was a author instance.