If a package contains more than one desktop file it should be listed several times in the package list. In the case of gnome-games I would have to remove mahjongg to get rid of solitaire.
In gnome-app-install we do so and show a little dialog, which says something like this: "mahjongg is bundled in a software collection. every change affects all other bundled applications ... see list below"
Sane. I'm going to rehash PkExtra one day this week, so we can make some things a little more sane when there is >1 app in one package.