I remember seeing flowers shipped by rail back in the '80s in Sanremo (a major flower growing city near the French border): they were packed in plain cardboard boxes. They were loaded on special boxcars placed at the head end of passenger trains. The boxcars were fitted with through cables for HEP and were certified to run at 120 kph (75 mph).
Some years ago there was an attempt to ship Dutch flowers by rail, using refrigerated 45' containers loaded on normal intermodal flatcars, but as far as I know it was not very successful and ceased operations after a while.