We have an enclosed carrier on top of the towed vehicle. We have a 12 gallon portable waste tank. We carry it in the car top carrier. I do lift it into the Jeep Cherokee to dump. I am actually able to pull it over to the Jeep on it's wheels, lean it against tailgate and then slide it into Jeep.
Nobody would try to store a full portable waste tank in a compartment. The larger ones with wheels are able to be towed with a vehicle with trailer hitch ball. so it can be towed slowly to a reasonably close dump.
The small ones are convenient. When we boondock on BLM land one day a week I usually make two trips to the dump site, one black water and one grey water. Sometimes two black water and one grey water. Bring back water in one 7 gallon and one 4 gallon water container. Then pump into motor home with 12 volt pump from harbor Freight.