zep101, this is a twofold question. First let me try to answer the "heatgun" issue. For that I would like to direct your attention to the "semi scientific" experiment Hair dryer for logic board reflow?. Yes, it does melt solder.
2nd part of your question is the why you are using the heatgun. It is a bit more intricate to explain. The key to this is the design of the GPU which is a flip chip design. The proper definition of that can be found at Wikipedia "is a method for interconnecting semiconductor devices, such as IC chips and microelectromechanical systems (MEMS), to external circuitry with solder bumps that have been deposited onto the chip pads." So what happens is that the chip heats up (due to poor design of the ventilation and heatsinks of the console. Does not matter if it is a PS3, a XBox or some of the Mac laptop's) and the bumps that connect the chip to the substrate lose contact and your chip (in this case GPU) fails. The heating of the chip for the reflow actually reshapes (most of the time) the bumps to the point of making contact again. That is the reason why some of the reflows just do not work. The connection between the IC and the substrate has absolutely failed. Not the most scientific explanation but I hope it makes sense to you.