Silverstone Cooling Pros:
Less obstructions in the airflow path (eg no drive cages in front of video\CPU, no PSU over expansion cards)
Air flow layout assisted by natural convection (heat rising)
Exhaust fan directly over video card
Fits larger tower heatsinks (165mm vs 130 mm)
PSU has decicated intake\exhaust vents so its heat is seperate from the system
In order for the cases to be on an equal playing field then the v354 would need to be running without the extra drive cage.. So taking that into account let me redo your silverstone pro's list..
Less obstructions in the airflow path (eg no drive cages in front of video\CPU, no PSU over expansion cards) no Drive cages infront of video cards, & unfortunitly for the silverstone it doesnt have a PSU sucking the heat off the expansion cards exhausting it out of the case.
Air flow layout assisted by natural convection (heat rising) Uhmm same thing applies in the v354 given that big fan spot right in the top of the case. Infact due to being able to take multiple fans in the top half of the case edge would go to the v354
Exhaust fan directly over video card Not sure what your talking about here.. The video card is exhausting itself upwards so there is no exhaust fan above the video card.
Fits larger tower heatsinks (165mm vs 130 mm) this is the only edge the FT03 actually has ve the v354 in cooling
PSU has decicated intake\exhaust vents so its heat is seperate from the system and you think thats a pro? That only helps keep the PSU cooler, not the rest of the system. Otherwise the PSU exhaust works to help suck heat out of the system. Especially when its up against hot components such as a video card.
And a Big difference not pointed out here is that if you were to attempt to run 2 large video cards in the ft03 you loose all your forced airflow over the video cards. As you would have to remove the fan in order to get the 2nd card in there.