I would guess each of these words has a different history and therefore the reason for the existence of antonyms is not unique. For example, sanction comes from a Latin root that meant "to decree, confirm, ratify, make sacred" (related to sanctum "saint, sacred"); that's the original meaning, while according to the source
Seemingly contradictory meaning "impose a penalty on" is from 1956 but
is rooted in an old legalistic sense of the noun.
The double meaning of off has to do with its original use; since off has the sense of "away, departing", go off was used for firearms meaning "explode, discharge". It's a kind of event that makes something work and also renders it useless for a while. When an alarm goes off, it ceases to work in a way: it has warned you of something, but it won't warn you about what may follow.
The verb cleave (another of your examples) comes from two different sources. At the beginning they were phonetically distinct and also conjugated differently, but then they coalesced, which is why they're used very little:
The confusion was less in Old English when cleave (v.1) was a class 2
strong verb; but it has grown since cleave (v.1) weakened, which may
be why both are largely superseded by stick (v.) and split (v.).
The infamous inflammable / flammable pair stems from a confusion between the Latin prefix in-, which denotes negation and comes from the Proto-Indoeuropean root *n̥- (the origin of negatives such as non, nec, etc.), and the other prefix in- meaning "into/upon", which ultimately comes from PIE *h₁én.
Auto-antonyms are not bizarre: they continue to exist as long as speakers are able to rely on context and common sense to distinguish between them, as pass out of fashion once they become a problem for comprehension. In this sense they're not different from other features.