I expect that a common use of an IT Pro creating a modification package is to add/alter settings that are in the primary package. Along that line, when I ask to create a modification package and identify the primary package, I would like to have access to assets that are in the package so as to modify them. The altered components, or those added under package folders/keys, would be overlaid on the main package when running in an environment with the package and add-on package.
One possibility is to take an approach like the App-V sequencer powershell "Expand-AppVPackageToLocalSystem", which extracts the file/registry items and lays them down on the system just like when the package was being created. Incidentally, I am guessing this is how "install" of a MSIX package on Windows 7 would work.
Once expanded like this, when in the installation mode of the modification package, all one needs to do is locate and update configuration files/registry items en-situ.