Again, I don’t have the level of detail available to me to answer in the specific context of the Avid software.
The difference between autoremove and explicitly adding an item to managed_uninstalls is that you can _remove_ items from managed_uninstalls (and therefore have Munki leave something alone!)
Scenario:
AvidNew is installed.
AvidOld is set for autoremove
If you cannot resolve that situation, having AvidOld set to autoremove would continually do the wrong thing, as it would also try to remove AvidNew.
Let’s look at this a different way.
Let’s say you imported Firefox-42.0 into your Munki repo and set it to autoremove.
Machines with ANY version of Firefox (even Firefox-43.0) will have Firefox removed, as removal is not tied to a version. Munki sees Firefox is installed and determines it should remove it. It sees an application bundle at /Applications/Firefox.app, and that tells it: yes — some version of Firefox is installed, so we need to remove it.
So much of this boils down to the pkginfo for all of the items in play, and whether or not Munki will see AvidNew as simply a different version of AvidOld.
This problem generally does not hit things like Office2011 vs Office2016 or Photoshop CS6 vs Photoshop CC2015, because these truly are different pieces of software that can be installed at the same time. They have different receipts and different application names or install to different subdirectories under /Applications.
-Greg