Just played a game where, to my surprise, Loner caused Toughness to trigger. I mean, come on! It's bad enough that Penetrating attacks trigger Toughness. But Blind Rage is psychic damage, just like Loner, and yet it doesn't trigger Toughness.... "This damage cannot be prevented by Armor." *Edited to focus on the topic of Loner.*
The penetrating keyword does, in fact, say "...unless that armor prevents all damage." (A rule which, presumably, exists so that you can't penetrate through Only Bones or other such special racial armor, and which just happens to overlap with Toughness.) But the particular behavior reported does seem like a bug, given that Loner says "This damage cannot be prevented by Armor.", just like Blind Rage.