Hi Erez,
1 - you can only create Service Apps in your org, where your login user is registered. If you have a user for the other org, then you can create a Service App using that user. Otherwise, the SA would need to request authorization from the Non-affiliated org, as described here https://developer.webex.com/docs/service-apps > section Request Authorization of a Service App in a Non-affiliated Org
2 - If you submit the Service App to AppHub, then it will be public for everyone, viewing audience cannot be restricted there.