Junkers are indeed the last in the chain. But not only.
Their rumours and base descriptions tell you that they're in the smuggling business as well. And those texts are even from vanilla FL.
And, basically, shouldn't you apply the same on a generic Smuggler? He as well should be treated unfriendly by Corsairs when scanned with Cardamine and vice versa. In my opinion, the Junker ID is a "better" smuggling ID.
Maybe it's just me not liking generic IDs though.