Loki-Midgard I think I misunderstood your initial question.
From your first post I understood that office too was deployed as an MSIX package.
Modification packages will not work if office is not installed using an MSIX package. The modification packages are specially designed to extend/customize existing apps that have been deployed using an MSIX. In that case, the modification package would add the registry entries in the context of your app, not globally.
However, this is not your case. A normal installation of Office will not "see" the registration from your application (installed via MSIX) because the registry entries from your MSIX are visible only to your application.
What you want cannot be accomplished with an MSIX. Apologies for the confusion.