Port installed options would be things such as running boards, different wheels, remote start, tow hitch, etc vs. factory installed such as power rear door, cold weather package with upgraded alternator, etc. The port is just a name that stuck around. As far as I know they are shipped from the factory to a central distribution point (the port) and from there are shipped to the individual dealers.

 https://www.toyotanation.com/threads/factory-vs-port-installed-accessories.752866/