Hi Qpsadmin,
Yes, you are right. We can manually set up the Organization Relationships manually in the Windows PowerShell. Please follow the detailed steps in this article: Create an Organization Relationship (Use the Shell to create an organization relationship) and check the results, if it doesn’t work, provide the error message you receive.
Additionally, based on my experience and the error ''Subtask Configure execution failed: Creating Organization Relationships', sometimes the firewall settings could cause this issue.
Have you deployed firewall (Microsoft Forefront TMG) or Load balancer?
Please make sure that the port 587 is open.
Thanks,
Bourne Zhang