FWIW, I used double wall from the stove connector to the ceiling support and it was triple wall insulated (class-A) chimney pipe from there to the roof sheathing collar and cap. The actual chimney technically started at my ceiling, so I have the big box right there.
IIRC Larimer County wanted to see 2" or maybe it was 3" from the blocking and sheathing in the roof to the chimney pipe. I can't find the building code reference right now, but as I recall Larimer didn't take any exception to the 2009 Code, which was in effect at the time. But, yes, there was a framed in box around the flue-chimney at the ceiling above the stove and a framed box around the collar at the roof. That's where the inspector took the distance measurements.
It looks like this at the roof jack, big collar, storm flashing over it.
I had to use double wall inside because they needed 18" minimum clearance for single wall to combustible material, which was violated by a partial divider wall in our room. With double wall the clearance was 6".
But I was going through an attic with insulation and did it by the book with an inspection, so my requirements were a little different.
ETA: If you were to take off the drywall on the ceiling over my stove this is what it would look like, with some blocking around the roof jack: