This is basically the definition we used. It's practically important because scanners really do miss software copied in via other mechanisms, and most of them give zero indication about it. For a few basic examples, try running your favorite scanner on the wordpress, node, or busybox images on DockerHub and see what the scanner finds.
For Wordpress, most scanners will miss that PHP or Wordpress are even installed in the image. The scanners spit out lots of data, but it's only about what they can find, offering the illusion of completeness or transparency.
Well then I guess scanners need to improve... I mean, the current version of Wordpress (and other software) is being made available as a Docker image because this is faster and more convenient than making it available via the package system, so it kinda makes sense that they are not available (or available much later) via apt/apk/whatever. Calling all other methods of distribution (pulling software from Github or via the various language-specific package managers) "dark matter" expresses the desire of not wanting to deal with that stuff, but surely won't make the "problem" go away.
For Wordpress, most scanners will miss that PHP or Wordpress are even installed in the image. The scanners spit out lots of data, but it's only about what they can find, offering the illusion of completeness or transparency.