A user has the addresses in the following order in Active Directory
When creating a stub object in the other organization for such user, the first company.com address is being used as the Target address, which in this case is John.Smith.firstname.lastname@example.org. This is not the primary address of the user and as result, the mail flow may be broken.
This is a known issue in QCS 3.0, it will pick the first address from the namespaces list, if there is more than one address from this domain.
This has been addressed in QCS 3.1 and later, upgrade to the latest version in order to resolve the problem.