Advice for planning our MSIX migration / Complex legacy application

JoeHae365  You'll probably get a better answer from someone at Microsoft, but here are a few thoughts...

Currently, Microsoft does not have a way for two separate independent MSIX packages to work together in the same container that is similar to the App-V Connection Group, although there have been hints that there may someday be that support.

MSIX does have the ability today for limited plug-in like packages, called dependent packages in some areas but known as Modification packages in the MSIX Packaging Tool.  These secondary packages cannot have shortcuts, so I'm not sure they work like you want.

Looking at the documentation you pointed to, you could probably change your approach to meet your needs, by implementing a single shortcut for the end user, and embedding access to restricted functionality by the presence of an add-in.  So everyone gets the main app, but only those users requiring the additional functionality having the extra package applied. 

Since you already are supporting plug-ins for other purposes, this might not be too hard. If you create a new "admin" plugin, it could be as simple as a button that launches a new process; you can even probably just use the admin exe as a file in that plugin msix package.  The key here is just in eliminating the extra shortcut and using the existence of the admin plugin package to provide access.

As to Protocol handlers, those seem to be working, but you'll have to test yours to be sure.