It was a line item to add or delete if you ordered a new truck.
Not many people were ordering new 80s built the way they wanted, most sales were just dealerships ordering stock, and they usually went for all the options. Higher cost -> higher list, more profit.
But yes, you will see these on occasion - no sunroof, no roof rack, cloth interior, non-sliding rear windows, aka "poverty pack".
Manual transmission: no. the platform was never qualified (think EPA/CARB) with anything but the 1fz-fe (adding a supercharger was CARB-accepted) and 4-speed auto.
Icebox: assuming you mean the center console fridge, no wasn't an option in the states
rear A/C: same. suggest adding a condenser fan. this was OEM on the 100, and the 80 series fitted with rear A/C