Trying to choke canvas, huh? lol Now that's a new one.
I'm thinking trying to cinch up the entire roof canvas so it closes up kinda like the top of a sailors duffle bag, won't be either easy or neat. My roof canvas was heavy, bulky and stubborn to work with. I'd bail on the duffle close idea.
What I did on my yurt was make the covers smoke hole the inside diameter of the roof ring. I sewed 14 loops to the seamed edge. I lashed the cover to screw eyes set in the bottom of the roof ring. It works great for holding the smoke hole in exact position, and keeps the cover from shifting or lifting in the wind. Plus it's a snap to lash up from inside the yurt.
Now, covering the ring hole. Hmmmm. It sounds like you're wanting to do something more sophisticated than cutting a stove pipe hole in the center of a metal trash can lid, and just letting the pipe center it atop your yurt. lol-
My idea is to make a traditional looking upper assembly seperately It would include the 3 quadrants of glass and one quadrant of stove pipe exit. Make it the same outside and inside diameter as the roof ring. Make the bottom flat, just like your roof ring. The whole shebang would need to be be water tight.
To seal the roof, align the upper glass and pipe hole assembly atop the roof ring and screw the two together. Or caulk a fat bead of silicone between the two before you sandwich them together.
Just thinkin out loud here. I've never studied how to seal the yurt roof. All I know is there's gotta be a better way than my trash can lid.