With the fixes in 1903, I can create a package with Notepad++, and then create a Modification Package to it that adds a plug-in dll. That is, I can do this and it works as long as I do not specify the installation folder while packaging.
But Notepad++ needs me to use the PSF in order for Notepad++ to see the customized configuration file (which is in the user's appdata area; without the PSF to perform a copy on access to the file it can't see the file). To use the PSF I must specify the installation folder while packaging or else the PsfLauncher won't see the config.json file as it must be placed at the root of the package and I can only do that if I specify the installation folder in the packaging tool dialog. Specifying this folder in both packages, the app does not see the plugin when I deploy the two packages.
I believe the fix added to 1903 is incomplete and needs to include this use case. Entered in feedbackhub with case https://aka.ms/AA5iy0i