Hi @jgriswold-moran,
Currently, users’ organization memberships are not included in the JWTs. Only the organization that a user is authenticating with will be present in the ID & Access token (including other claims associated with that membership like permissions).
That being said, there is a Management API endpoint you can use to get a given user’s Organization membership: Retrieve User's Organization Memberships, but it is not often recommended to call the MGMT API from within a Rule due to rate limiting concerns – at a minimum code defensively in case of rate limit exceeded. You can also call that endpoint using a confidential m2m client as a proxy to the MGMT API from your application. In addition, a user could potentially have a huge number of organization memberships, so it might not be feasible to cram all of that into a token.
Re: associating Auth0 Application w/ Auth0 Organization – yes indeed there are. Tell me more about your expectations there? Do you generate an Auth0 m2m client for each of your customers currently?