Alex, floor tubes, also known as a floor well, were usually large pieces of pipe hanging vertically down from the car floor, in which tie down chains could be stored out of the way. Easily modeled with a piece of styrene rod glued to the underside of your auto boxcar. A close look at auto boxcars undersides will show the tubes hanging down.
The AAR Pamphlet #28 you cite must be a much later version. The one I have is for “Methods for Loading, Bracing and Blocking Carload Shipments of Cast Iron Radiators in Closed Cars” issued Oct 1936, Revised Jan 1942.
In 1949 the AAR pamphlet #1 addressed “Motor Vehicles Shipped Carload in Auto Loader Cars” ie the loading of automobiles in loader equipped boxcars.
There is no #28 in the current list www.nscorp.com/nscorphtml/ncsc/aar_car_loading.xlsx