Narrow Gauge COFC and TOFC
The WP&Y carried intermodal ore containers (came from Mayo by truck) in their last years of real common carrier service. So narrow gauge intermodal traffic is (was in the case of the White Pass Route because the folding of the mines meant end of viability for them) in operation around the world. Unfortunately, in North America , I think the narrow gauge portions of any routes with TOFC (e.g. Mexico), have been either regauged if they had the freight traffic on the line to sustain operations , or have been abandoned.
While no one used Little River Lumber 2-4-4-2s in North Amrican intermodal service , and the WP&Ys mikes and the modern 'HR-01' class , NdeM three foot gauge , 2-6--6-2 s were far more modern and powerful locos ; those 2-4-4-2 loggers did haul around various pieces of self propelled vehicles, skidders, woods trailers/wagons, and camp buildings in the real world so why not containers on a model railroad. The Australians and Europeans have some specialized container models not made by Canadian/American mfgrs. which might be of use for your purposes. Both have prototype narrow gauge operators hauling freight containers of many sizes and kinds on a current basis.
Good-Luck, and keep on steaming, PJB