The idea is simple: add the "LINK" type of archetype to allow linking concepts and use those LINK archetypes in AQL to query the relationships. This can help to implement querying data and context, e.g. I want to query LINKs that link Problems and Lab Test Results, and this can be done in AQL. Without the archetype, this query can be done but in the traditional way, depending on a specific database technology (SQL, XQuery, ...).
A similar idea might apply when there are relationships using OBJECT_REF like in FOLDERs referencing items, and we want the FOLDERs that contain a COMPOSITION defined by archetype XYZ.