Actually, there are three places where links can occur.

1. There is the top-level links as in pagination. You can add additional links by either creating your custom pagination class derived ofrest_framework_json_api.pagination.JsonApiPageNumberPagination and overwritingget_paginated_response or you have a custom renderer derived fromrest_framework_json_api.renderes.JSONRenderer overwriting render method.
2. There are links which are part of the resource. Currently, there is no easy way to overwrite it and you would also have to have a custom renderer overwritingbuild_json_resource_obj.
3. Last, there are links which are part of the relationship field itself, which can be customized with a customResourceRelatedField overwritingget_links.

Hope this clarifies what is possible in terms of custom links.