Some airlines subcontract their freight operations out to third parties in order to keep costs down. The aircraft may be in the airlines colours but it’s a completely separate operation, typically with non unionised pilots.
Where the cargo operation is part of the airline, normally there is no differentiation in rostering, though obviously if the aircraft types are different such as B747 freighter with no passenger version then the crews will only fly freight.
Some airlines try to separate the operations and reduce pay for cargo pilots but typically offer earlier promotion to Captain to entice people across.