The Alternate SSO Domains option will only appear when the default SSO Domain that is selected has the Authentication Protocol set to LDAP. It does not matter what is selected for the LDAP Protocol under the LDAP Configuration Endpoint.
Additionally, the domains that will become visible under Available Domain(s) or Assigned Domain(s) will be those that have the Authentication Protocol set to LDAP.
It’s important to note that we match Alternative Domains on the name of the SSO. For example, a user who types their user name in in Username (domain\user) format will only match on an Alternative Domain called Domain, but not on Domain.com. Alternatively, users who type their username in Principal Name (firstname.lastname@example.org) format will only match on Alternative Domains called Domain.com, but not on SSOs labeled Domain.
If users log in using both formats, then one of each need to be created.