Well, in accordance with the lore covering up the RNG.... The cryptarch just decodes whatever the hell you have, he doesn't create it out of the engram. Think of someone who opens your lunch bag for you because ziplocks and brown paper are devil spawn: he isn't making your sandwich or juice box, just helping you reclaim it from a container. You'd look like an idget blaming him for you getting mustard on your wouldbe pb&j when he had nothing to do with that.
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Then why does he have a higher likelihood to decode legendaries the more you level him up, or rather your rep with him?
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Change in the RNG to give slightly higher biases towards specific gesr.
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Humans need to blame something for their misfortune.
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That's why Awoken stay clear of 'em!