It means the opposite. Since it’s the default behaviour to have these templates remain installed, this is what IPS expects and approves.
Before 4.5, templates were delivered separately and had to be installed manually. Since that is not possible anymore, since all Marketplace offers are now just one file, templates now come with apps and plugins, but they behave as before.
It’s not about the app/plugin that installed it. It’s about the name of the template. If names match during the upgrade, there will be conflict dialog which gives the user the choice to update the template or to keep the old one.