wrong, I had the modded version of a set piece equipped (and yes, I got it from a crate - aka random drop) and guess what, I got it again from Kai... and again, so no, it is definitely NOT working
I haven't personally experienced any duplicates, but that does not mean they don't happen.
Anyway, I still think it's important to explain precisely how duplicate protection works (should work), because I'd bet a larger amount of credits on that a majority of these reports are complaining about this erratic behavior and not an actual bug.