Adobe Shared Device Packages Overwrite Installed Applications

Hi folks, I've tried finding specific answers to this but it's not super clear. In a user-license model, we deploy applications to users to be able to install themselves, so it's not a big deal. For Shared Devices (We are an educational institution properly licensed for it), we have an issue where when we package an application and deploy it, if requirements for the machine change and we deploy a second package to it, it overwrites the applications installed by the first one.

For example, a lab wants Photoshop. We install it. Halfway through the year, they decide they also want InDesign next to it. If we deploy the InDesign package, it uninstalls Photoshop and only leaves InDesign. This makes sense as packages detail how something should look in its final state - the InDesign package only lists InDesign, so it removes Photoshop. However, This breaks down when we need to make a package additive, rather than replacing. 

Is there a better way to do this? We make packages with the three most common used applications are, but when we need only two of the three, we have to manually do it, or make piles of packages, each with the exact combination of shared applications that are needed. so nothing is removed when it's installed.

It should be easy. If someone wants Photoshop and Illustrator on a machine, we deploy the Photoshop and Illustrator packages. But we have a real issue handling an explosion in packaging simply beause shared device packages don't let you 'add' a program to existing installs.

Am I missing something? We need to do this in an automated way.