The railroads did and still do ship containers on flatcar but a double-stack? Not likely.
Except, that's not a container on flat as such. It doesn't go anywhere except back and forth on the CN.
That's a Distributed Braking Car, a dedicated car used to help maintain air pressure in cold weather. There's a generator, compressor, fuel and air tanks inside the old container.
"The March 2009 issue of TRAINS contains an article by Dan Calabrese on new technologies in use on the CN in Canada; where there are Distributed Braking Cars. These cars are used in flat terrain to facilitate longer trains without using additional locos as Distributed Power. The cars resolve a winter problem of very cold weather, shrinking gaskets, obviously a real problem on the Canadian plains."