Hi Swatto,
To answer the question:
Based on my research and knowledge, the federation metadata URL can only be used to retrieve information from Office 365 for the Relying Party Trust (RPT). Moreover, establishing the RPT with the federation metadata URL should not modify the SSO settings on the Office 365 side.
Meanwhile, in this case, although the RPT can be established in the ADFS 3.0 server, it is not an officially supported scenario.
Currently, to set up the federation trust between the ADFS server and Office 365, the only officially supported way is using “Microsoft Azure Active Directory Module” to run the related cmdlets. However, if using this way, the current ADFS 2.0 server cannot be used for SSO any longer.
Briefly, the officially supported way breaks the current SSO deployment with the ADFS 2.0 service. Although the RPT can be established in the ADFS 3.0 server without breaking the current SSO deployment, if issues occur after starting this deployment, official assistance may not be provided.
Thanks,
Claud