While went through more resources, I got more idea about the usage of system. It's depend on how we use witth different sub resources. For example under patient identifier, system value define how the identifier value created. With this it's should be Ok to use the patient identifier type uuid as urn which define the definition on how to create the identifier.
On the other hand the usage of system value under contact define which form of contact number is that. So it depends on the usages.
Please add your thoughts if I misunderstood the usage of system value.
Thanks,
Harsha