Have discovered that the related relationship routes are not merging the relationship links into the top-level links member. This does happen for the self relationship route, and should also happen on the related one.
The cause of this is the response objects are using the encoder's withResource() and withResources() methods, which return a standard compound document rather than a relationship docuument. Hence the links are not merged.
Fixing this will be a breaking change, as the following methods need to be added to the encoder interface: withRelatedResource() and withRelatedResources().