Some MTs do have a pump and will be damaged by flat towing. If your manual says no, I would go with that. I can tell you my Jeep Wrangler has to have the transfer case in neutral and the trans in gear to keep the input shaft on the trans from spin get.
You might check out
http://www.ford-trucks.com for more on this but I think you have your answer.
You can always drop the drive shaft, which shouldn’t be a big deal on that truck.