I set my question to Kentico support and received the following answer:
Thank you for your message.
I have checked with our development team and they recommend not using the object relationship. It was added to Kentico as a draft of basic functionality but in the end did not turn out to be as useful, and never finished. So for example it will not stage. It is currently scheduled for removal in one of the future major Kentico versions. Using custom table to store your relationships is the best way how to implement your functionality.
Please let me know if there's anything else I can do for you.
E-Commerce Senior Support Specialist