Port may be the correct word but gives wrong connotations. Vehicles are not shipped directly to the dealer from the factory. There are regional distribution centers of the country that Toyota sends it vehicles to. At that facility (which I called the 'port' since some -used to be all - Toyota vehicles are received on the coast) several factory items that appear on the sticker are installed. For instance, on my windown sticker it lists the Toyota bug shield. That is not installed at the factory in Princeton. It is installed at the 'port' or distribution center, not the dealer (unless you wanted it and it wasn't ordered that way or you were buying off the lot) . I had several options installed at the port so my truck matches what is spec'd on the window sticker. There are many other 'port' installed options as noted at
edmunds.com. Another are the door sill protectors.
I might question your dealer a bit more or contact Toyota to validate the answer if you are curious. It sounds like they may not be ordering a vehicle for you but finding something in there allocation that matches but was ordered without the shell. A true order build will come through the port with port options installed only at that location. I would prefer that scenario since there are likely strict instructions on how the wiring is done, what clamps are used, etc. I would imagine the dealer stands behind vendor work but I wouldn't care for it. If you had a problem I imagine the dealer would pawn you off the vendor. You'll know if its a factory option if it appears on your window sticker.
So I picture your shell being shipped to a vendor by SnugTop, then trucked over to the dealer by the vendor and then placed on your truck. That's a lot of fork lift moves. Sounds mighty inefficient for a company like Toyota. Who pays the vendor? Sounds fishy to this jaded nose. Please correct if wrong.