The manifest is the paperwork that includes the car number, the product or merchandise on the car, the shipper, and the receiver of the merchandise or load. It may also include a different pick up address or delivery address if those addresses are different than the shipper's or receiver's billing address.
It is not so common now, but in the days prior to the completion of the interstate highway system that resulted in freight being transferred from trains to trucks, there was also lcl or less than car load freight where a number of shippers would bring freight to a freight warehouse owned by the railroad and freight going to the same destination city would be combined on a single freight car bound for a similar freight warehouse in a distant city where the car woudl be unloaded and the freight distributed to individual receiver's.
In the old days, the conductor would receive a stack of manifests for all of the cars on his entire train to be turned in when the cars reached their destination.
I think the term "manifest freight" is actually a redundancy, since every freight is a "manifest freight." In practical terms, some unit trains may have identical manifests for every car in the train excepting the car numbers because the entire train is loading in one place from one shipper and being delivered in another place to a single receiver.
I suspect that the "manifest freight" refers to a train where the various car loads are picked up from different shippers and/or delivered to different receivers.