When Scribunto requires a file from an external package, it should register a link of some kind. This is Scribunto's responsibility, not Produnto's.
@cscott proposes to use pagelinks with a title that can exist but doesn't, analogous to a MediaWiki namespace page for a default message.
It would be possible to add a new link table, but this would mean a lot of hooks, and an extra table for every wiki. Scribunto doesn't currently have any SQL tables, so it adds some installation complexity.