1. Enable auto-account creation within portaladmin->security->config-> Update Security Configuration
enableAutomaticAccountCreation":true
This allows the enterprise user that belongs to the other domain to automatically be added to Portal for ArcGIS.
2. Upgrade to version 10.4 and specify the domain controller that acts as the global catalog in the portaladmin endpoint:
http://server.arcgis.com/en/portal/latest/administer/windows/configuring-the-domain-controller-used-by-portal-for-arcgis.htm