From a browser perspective, it is going to send all cookies to the server which match the domain (Persistent and non Persistent). Thus I believe when you SSO across the federation partnerships, those partnership should be able to see the SMSession.
I don't know the use case which is prompting you to set SMSession as Persistent Cookie for a federation partnership. I have never seen anyone needing to make SMSession Persistent Cookie. I hope you understand the risks of making SMSession Persistent Cookie.
What I'm not sure is would there be a conflict between a Persistent SMSession Cookie and nonPersistent SMSession Cookie, when either CA SSO component (where PersistentCookie=YES VS NO) issues a SET Cookie to browser.
Since you have the setup test it and investigate the following.
- fiddler traces.
- webagent trace logs.
This would give a better picture of what is transpiring in the entire flow.