I did not know that about the default updatenotification module. Good to know.
I have that module in my config.js with no config options, so I am running the default options. And I have not seen it put up a notification if there was a newer commit on one of the modules (which was the case). In my case that one module that had a newer commit was in my modules directory but not used in config.js, so looking at useModulesFromConfig option, I assume that module was not looked at. So it all makes sense.
I did put in a pull request to tweak wording in updatenotification.md
Cheers