Superhot chilli belong to the species Capsicum chinense.

Varieties that belong to this species tend to produce more capsaicin, and therefore spicier ‘pods’, anyways. (But note what is also said in “Is all chilli spicy?”: Not even all Capsicum chinense are hot, some are mild.)

In the superhots, there seems to be a mutation (a difference in their genes), too: Normally, capsaicin is only produced in the placental tissue of the fruit (the part that the seeds are attached to).

The superhot types of chilli, however, have capsaicin-producing cells not only in their placental tissue, but even on their fruit walls!

So, superhots produce capsaicin all over the inside of their pods!

Source: Paul W.Bosland, D. Coon, and P.H. Cooke. Novel formation of ectopic (nonplacental) capsaicinoid secreting vesicles on fruit walls explains the morphological mechanisms for super-hot chile peppers. Journal of the American Society for Horticultural Science 140:253-256. 2015.