Factory installed options are those installed during the factory build in Japan or Cambridge Canada. Port refers to dealership installed items, floor mats, luggage rack rails, maybe remote start and a bunch of others.

 

If you are in the Southeast US..... Southeast Toyota (SET) likely had a hand in any port added options.

I've lived in the Carolinas for almost 25 years. The new Toyotas I purchased since 2004 had a SET fee on the sticker, and may still, I have not bought anything new since 2014. Many items/options added before they are ever sent to the final dealer, like the items you mentioned. Basically a middle man. In my experience anything added at the "port" was added by SET in this part of the country.

Southeast Toyota Distributors (SET) serves as the exclusive importer and distributor for Toyota Motor Corp.'s products, including Lexus, in their specific region.
Geographic Area: Their territory covers Florida, Georgia, Alabama, and the Carolinas.
Scope: SET is responsible for handling the importation and distribution of a significant portion of Toyota and Lexus vehicles to dealerships within this region.

The "SET" fee on a Toyota sticker refers to the distributor and their region. Southeast Toyota (SET) is a major independent distributor that processes and adds regional charges and accessories to vehicles before they are sent to dealers in the southeastern U.S..