It was pouring rain, the drainage from the runway was poor, the runway is very short and the pilot tried to stop, but in vain. Having landed and taken off many times as a passenger from that airport (Congonhas), including a number of aborted landings due to pilot failure to hit in the first 1000 feet, I do not blame the pilot, but the runway length and the weather. There have been many crashes there. This was the worst. It’s the scariest airport I’ve ever seen, where planes land and take off, flying very close to tall buildings, not to mention the sight of the short runway when your are landing there.
One thing certain, that the very last recording listed at the link cited is quite strange (all your explanations notwithstanding).
Absent other information, I think you assessment is accurate. As far as scary airports, try Queenstown, New Zealand.
Not only that, but why would a gas station be allowed near the end of the runway even if it is on private property?
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ahem...try the (old?) airport in Huntington, WV...landing there '84, 737 pilot had to "stand on the brakes...rainy/morning/short runway...burnt wrecks next to runways...long ago.