Munki is designed to check for blocking apps and prompt for them to be manually quit by the user.
Sadly users are notorious for not paying attention to things like this. Munki does progress to then effectively blocking access to the rest of the Mac as way of 'encouraging' them further but again a lot of users will not know what to do. Furthermore some 'apps' actually are not straight forward apps in the dock but applets residing in the menubar which again many users cannot comprehend. (Even some 'normal' apps do not 'quit' when the last window is closed which is considered to be the standard practise on a Mac but not on Windows and some Mac developers follow the Windows standard instead.)
(As an aside disabling Microsoft Auto-Updater is a very good idea to stop it acting as a blocker.)
For other apps, particularly various menulet based apps e.g. iMazing, 1Password, possibly Tunnelblick, etc. it would be possible for an admin to write a script which could automate quitting these before Munki then does an update and then a similar script to relaunch them after Munki has completed the update. However as far as I can see there is currently no mechanism in Munki to facilitate this.
The current pre and post scripts only get triggered if there is no blocking app - duh! In this case they need to run specifically because there is a blocking app.
Note: I am not suggesting this approach be used for e.g. quitting Microsoft Word but I am opening this for discussion in relation to types of apps a user might find more confusing to deal with.
What do Greg and others think?