In one of my annexes I will g-a-add a (e.g.) zip file, extract and g-a-add its contents and then set metadata on "each side"..

git annex metadata -s extracted_from+=$ files_from_zip/
git annex metadata -s extracted_to+=$key_for_file1
git annex metadata -s extracted_to+=$key_for_file2
git annex metadata -s extracted_to+=$key_for_file3
git annex metadata -s extracted_to+=$key_for_file4

This means that if the content for a file in files_from_zip/ is lost, you can easily find that it came from (which may not be lost) or any other zip in that annex that also contains that file.

I was wondering if this would be worth building in?

git annex metadata --fromto files_from_zip/

There are other situations this is useful (and I use), for example, when I convert an annexed file to another format, I record the "source" and "target" keys against each other. I suppose a very general name would be:

git annex metadata --parentchild files_from_zip/
git annex metadata --parentchild original.wav compressed.flac
git annex metadata --parentchild original.svg compressed.png

and this would set 'parent' and 'child' metadata respectively.