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And yet somehow, as far as we know, the energy of every molecular collision is faithfully preserved during a supernova, when effectively the entire volume of a star collapses into its core in less then a second.

Reality is very strange.

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That's not accurate. Only the inner core collapses (hence the "core-collapse supernova"; there are also other types), the rest rebounds, is heated up by core-produced neutrinos, and gets ejected. The Wikipedia article is a good start, also there are plenty of good papers on arxiv (e.g. on still-not-too-successful numerical modeling of the aforementioned "heating", without which the thing simply doesn't go bang).

Good correction, thank you!

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