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I'm pretty sure that choice of augments only applies to the final body armor reward from those missions. The augment system for every other piece of gear comes from random drops from ANNM or the elite training regime if you trade a piece of gear (50 or under) and kill the NM. Even then the augment won't necessarily be good or worthwhile.

Be careful when trading, since you'll lose out on being able to sell/trade it back.