No need to apologize for anything, I would have probably said the same thing lol. Like you said the agent told me they don't know why they update with messages not related to the updates did on the system and they have been getting a lot more calls about these ghost updates.Great that you found this out.
BUT and apologies for this: it's a new system and they're changing things and we don't really know what these messages mean (as you put, they're not necessarily related to what was done). So I'm not clear what the use of worrying about it or spending any time on it.
Or most simply: not clear to me how much use or if reliable conclusions can be drawn from these messages.
So far - hopefully they'll update and make it more transparent, and the functionality just isn't there yet.
Hopefully the new tracker gets fixed soon and this may lead to less phone wait times.