I think it's just done by voting, anyone could submit an alternative link, but it would need X upvotes to be promoted to the primary link.
I can see how this might not work so well with contentious stories, but when it's just linking to the primary source vs a poorly written article on a secondary source it might improve the experience.
This is also true when something is paywalled but there are alternative versions.
Edit: In my mind it's an additional facet, rather than just being done in comments. Maybe it's not even visible unless you're a high karma individual.