Yes.
A single entity can have multiple systems, and each system can be scoped and audited independently.
For example, an organization might have:
A custody platform
A trading or exchange system
An internal treasury system
Each of these could be treated as a separate system if the key management processes, infrastructure, or teams differ.
Each system would:
Define its own Trusted Environment
Be assessed against CCSS requirements
Receive its own certification level
This allows organizations to certify specific parts of their environment without needing to include everything under one scope.