If you see Apple updates (that require a reboot) not installing properly via Munki, it may be because the downloaded update is stale somehow. Not really 100% sure on how this works, since I've seen this fail even on a "stale" update downloaded the same day (not weeks ago).
When you log out to update, you'll see Munki's progress bar over the login screen window, and it will look for a split second as if it's trying to install the pending Apple update but then move on almost immediately to requiring a reboot.
Then, if you check the logs at /Library/Managed Installs/Logs/Install.log, you'll see something like
You could create a script (run from its own Launch Daemon or as part of a Munki run) to clear old updates from the /Library/Updates folder periodically (though, again, I saw this happen even with a recently downloaded update).
I've found that if you run
This is tricky, because it's not technically a Munki issue (Munki just uses Apple's built-in softwareupdate to install Apple software updates), but clearly there's some flaw in invoking the software update mechanism.