I’ve been mixing it up: some of what you are doing (it hasn’t consistently given the augments You got lucky getting two! 
), doing Nexus missions that give augments as rewards, and claiming crashed ships and scrapping them.
I don’t know if you noticed our Crashed Ship Registry started by @Polyphemus: Here is the link just in case: Synthesis - Crashed Ships Register
I’d be interested to see how it works out for you in future on a larger sample. Lets say, 20. And see what the % of Augments that you get only from that sample.
Hopefully your luck will hold! Two! from a low level ship. lol So lucky! 
Thanks for sharing!