If you join ISE to a domain it can talk to all the other domains in that forest and any domains with a two way trust. You should be able to map in groups from those other domains and use them in your rules. You typically don't need to join the other domains specifically.
I think I have a similar scenario. I would like to have a second join point to the same domain with a different set of groups to use in an authentication sequence for the MyDevices portal. (I only want a specific group of users to utilize the portal.)