Please treat the following a FUD, or read really carefully and try to understand what I am trying to say. (I know it is extremely hard, but try.)
We all assume that the material used by the cover is non-flamable, but the pictures showed that it is. Normally, plastics are flammable due to its chemistry compound. Again i'm not a chemist but I believe there are no ways to make plastic "fire resistant", only "fire retardant". However, making it fire retardant means it is hard to cut. If, and I mean 'IF', manufacturer chooses to cut corners and use fire resistant coating instead, then when plastic melted, it may become flammable.
It doesn't take a lot of heat to melt the cover, only about 90-120 degree. If there is a source which keep a single drop of plastic in its liquid state, the chemistry compound can change as things may evaporate, turning that single drop of plastic a fuel for fire. If that is the case, then you actually have a mini bomb sitting at your PC waiting for a chance to ignite. It is hidden underneath the video card so it is really hard to detect. It is sitting on the hot source which is keeping it in liquid state or constantly changing its states (that sounds fun to a non-chemist like me).
My theory is flawed because it takes some 300+ degree to ignite plastic which is not really possible from the heat off HS, but my theory does favor the above assumption, keeping a drop of fuel on top of the NB HS. My guess is, the whiter spot on the NB HS was the spot covered by melted plastics, and eventually ignited, burning the plastic on top of it, creating the dent at the cover. The temp of the ignition was so high that melted plastic turn into fuel, yet the resistant coating from new plastic prevented it from burning repeatly. Yes, the question is what triggered the ignition.
If what I said is plausible, then the entire case may not be user fault after all.If there is a drop of fuel sitting on the HS surrounding electronics, then a single spark or discharge can indeed ignite the fuel I.e. a discharge from video card towards the NB HS. The point where that drop of fuel seats must be the point which the HS is closest to the cover and therefore the point where a discharge will occur, just like how a lighter works. In OP's case clearly something was ignited. In fact, the temperature of the smoke what so high that it caused the shroud near the fan to melt as it sucks air in. Evidence of extreme temp is clear. Look at the PCIe pins off the 2nd card, only temperature over 300 degree can cause that kind of damages, and it is from the ashes resulting from the plastic burn.
I don't think anyone would have even remotely imargine that the cover of the video card can turn into fuel. Even if there is a chance it is a big deal. There is a big difference between "not possible" and "highly unlikely". By looking at those pics, it really isn't as simple as a fried chip or a pop out resistor. It can kill, especially running SLI/Crossfire 24/7 unattended + poor cooling. Chance of winning a lottery is low, but someone will win. If the above is plausible, then we all should really place a fire distinguisher right beside computers.
Again, I have no proof, data nor the expertise to make this as a claim. At best this can only be a plausible case. If OP wants to get to the bottom of this, please follow idontcare's advise.