You should rely on configure for enabling features. configure checks if the dependencies for a plugin are available on your system and will build plugins having all dependencies available.
If a plugin is not enabled, it means it requires some libraries that are not found on your system.
If you don’t need any of these plugins, you can ignore it and use available plugins.
If you need one of these, you would have to find which dependencies are missing and try to install these with apt.
Having installed the gstreamer plugins good, ugly and bad for standard version from apt would probably have installed most of the useful dependencies.