Yes, it's designed so that only you and Mercer can encounter Karliah, and is a Thieves Guild zone.
It was a bad move on the designer's part to also use it for the Jarl's quest.
I guess my plan won't work, then. Especially since it happens again with the eye of the falmer. I wanted to have my follower steal all of the quest items, so that if I decided to complete the Thieves Guild, I could hopefully wait for a patch and then take the items from them to start, and then complete, the quest. That's the key, as if the follower steals the items, the quest doesn't officially start. I did the same thing with the glitched musical bard items.
But as I've said, it's a moot point, since two of the items are in areas where followers can't go.