We've historically had a custom "third party relationship" object in our Org to handle scenarios where a Contact belongs to one Account, but has a relationship with another Account (or child record thereof).
This has been handled by having lookup fields to Account, Contact and the third-party object - a Contact can be related to another Account and/or the child object.
We're now investigating moving to the the native Account Contact Relationship functionality (https://releasenotes.docs.salesforce.com/en-us/summer16/release-notes/rn_sales_shared_contacts.htm) - because, in theory, native platform beats custom implementation.
However, we cannot add that third lookup field to the child object - there's just no Lookup option available on the Add New Custom Field dialog. Assuming this is by design, would the only way to achieve this structure be to continue using our custom object?