Hello Rahul,
Please, find more details on this topic in my blog if you decide to use Kerberos:
Kerberos/SPNEGO for SAP AS ABAP in a Multi Domain Environment.
If you decide to use X.509 certificates with Secure Login Server, you can configure these two different domains as users store for AS JAVA and the scenario will be also working. Here you have a requirement for unique userIDs across both domains.
Regards,
Donka Dimitrova