I was looking through the new API for plugin installation (and other Modify2 methods), and one comment I have is that letting the apps create the startup notify id means that true startup notification is impossible (because the app does not know the desktop id of whoever is responsible for installing the plugin, gnome-software or apper or whatever).

_TIME%d is enough to fix focus stealing prevention, but does not offer feedback for app launching, which means that the user will be staring at nothing happening until finally gnome-software launches (which can take a while, given the amount of IO g-s triggers through PackageKit).

Instead, the PackageKit plugin should create a real startup notify id (with g_app_launch_context_get_startup_notify_id()), using the timestamp provided by the application, and pass that to Modify.
This will make sure that even if gnome-software or apper slow to launch the user is aware that something is happening.

As for which desktop file should be associated with the startup notify id, given that multiple providers for the Modify2 interface exists, I'd say it can be fixed with DE detection or with a configuration file. After all, you cannot install apper and gnome-software at the same time because they offer the same DBus service, which is not allowed.