The question does not seem to be sharply formulated, so the answer will be vague: "super" comes from the way semantic evolves. Words have antonyms, usually conceived as negations, but negation can have different modalities, so instead of a pair, language usually has more terms. This idea has been developed in the semiotic square proposed by Greimas. So we have e.g. 'natural' and 'unnatural' but also 'artificial' and more over 'supernatural'. In science: symmetry and asymmentry and anti-symmetry. I doubt that linguistically supersymmetric has any relationship with supernatural, but one has to know who first started using the word (and here we might recall the history of the 'god-particle').

The question does not seem to be sharply formulated, so the answer will be vague: "super" comes from the way semantic evolves. Words have antonyms, usually conceived as negations, but negation can have different modalities, so instead of a pair, language usually has more terms. This idea has been developed in the semiotic square proposed by Greimas. So we have e.g. 'natural' and 'unnatural' but also 'artificial' and more over 'supernatural'. In science: symmetry and asymmentry and anti-symmetry. I doubt that 'supersymmetric' has any mental relationship with 'supernatural', but one has to know who first started using the word (and here we might recall the details behind the famous 'god particle').