There are times that two applications integrate together, but not using a "plugin" style integration. Both packages would contain executables and shortcuts, but the second app uses "stuff" from the first package.
The connection groups in Microsoft App-V are good for this situation of packaging separately and deploying as a single (layered) environment. Because vendors don't usually release in AppV format, we can also package both into a single package if we want.
If the primary app vendor releases in MSIX format, we never want to edit that package directly. So it would be preferred to package the secondary app up separately and reference the first. The Modification package doesn't work as it doesn't capture shortcuts (and probably other entry points). But even if it did I'm not sure launching a shortcut from the add-on package would cause layering to work correctly.
If you need examples of such apps, look no further than apps with EXEs that integrate office components like Word and Excel.