If you really get into operational considerations of TOFC, don't forget the various intermodal "Piggyback Plans" that were around back in the day, as discussed in this thread (wherein Greyhounds expresses his appreciation for ICC regulations ). For a slightly more structured discussion, this Google Books excerpt from "Practical Handbook of Industrial Traffic Management" (1987, but it reads more like it's from 20 years earlier) could be interesting.The only real effect I could see those plans having on a layout is the ownership (and names) on the tractors, trailers, and TOFC rolling stock.
I did not see a direct reference to NYC's flexi-van service, but here are some links to check out:
https://www.flickr.com/photos/jnos363/5082152589
http://rrmodelcraftsman.com/reviews/cm_extra_walthers_flexivan.php
I dont think that Walthers produced the 6th wheel Yellow tractor (called a Commando by NYC). They did make the Flexivans themselves and possibly the trailer bogies. Check out this thread for an idea on how to kitbash the commando:
http://cs.trains.com/mrr/f/13/t/246384.aspx