I just want to make some observations here.
Regarding the matter of placing the cards in the 1st & 3rd PCIe x16 slots, those are the only full x16 electrical slots on the board. The 2nd & 4th PCIe x16 slots are actually x8 electrical. For full x16 links to both cards in SLI you have to use the 1st & 3rd slots. This is true for many other motherboards. Also for 3-way SLI the cards have to be sandwiched. nVidia-supplied 3-way SLI bridges require that the cards are sandwiched, and some 2-way SLI bridges require that the cards are sandwiched. Therefore while we could say that this is not an ideal configuration (especially for the top card) it is certainly a fully approved and expected configuration by the hardware designers and manufacturers.
I don't see how the southbridge heatsink could possibly get hot enough to help start a fire on the cards or the board. That just doesn't sound possible to me. The board would have shut down due to electrical problems before that happened I would think.
I'm no forensic scientist, but it looks to me like flame shot out from the lower x16 PCIe slot and burned the back of PCB of the lower card and the heatsink shroud of the upper card. A sudden massive short in the lower card's PCIe slot which caused an intense electrical fire before the computer shut down? It's not at all clear that the card itself is specifically to blame. The OP could just as easily be requesting a new board from Gigabyte.
I'm too no forensic scientist, but I personally found this case extremely interesting.
I see what you are saying and agree. Those HS shouldn't be hot enough to ignite as they are attached to a chip with some thermal production. However, that doesn't mean they can't emit heat beyond the temp which will trigger the production. For example, have a heat gun can heat up things that can exceed the temp of the gun itself. Assuming the air flow is dead, heat could have radiated off video HS onto the cover from inside, while outside the cover is touching the NB HS, which again become to junction point of 2 source of heat. Yes, even than it shouldn't ignite, but possibly hot enough to melt stuffs, i.e. plastic in around that area, which is the setup of the incident. By looking at the clip of 4th PCIe, it is clear that de-shape(melting) is the result of pure heat, not fire, as there are no burn marks. Yet, the 4th PCIe was so far from the point in question, if the 4th PCIe de-shape was due to the point of ignition, then we can see how hot it must be at the point of ignition.
Heat may not be the caused the ignition. As you suggested it, may probably be a power scourge coming from the 2nd PCIe slot. Look at the 2nd PCIe, it is de-shaped so bad that the socket itself isn't straight. It is possible that those pin were touching each other within the connector, which caused a short so intense that it actually ignite the cover.
However, if that is the case, then the 2nd PCIe socket should be melted too. Look at the melted cover, there is a dent at the location away from the PCIe slot. Coincidentally, that dent is on top of the part where the NB HS white spot. My guess is, the card actually melted before the ignition through time, and the part melted onto the HS actually trapped heat, and therefore ignited. I'm not a chemist either so i don't know the ignition point of that type of material, all I know is that type of material produce huge amount of smoke which actually extinguish the fire upon ignition.
Of course, my assumption is the dent is where the ignition occur, but that doesn't explain the mark underneath the fan.