Not sure I fully understand your plan, but when I installed a 17k btu sigmarine heater in my W36, I put it on the forward bulkhead. The hole was slightly smaller than recommended so I could install a Nicro vent down the road. I think the stove pipe was 3 inch, and I drilled a 4 inch hole in the deck.
In the end, it didn't draw well even with added lengths of stove pipe. Smaller hole for the stove pipe was not an issue.
Good luck. Hope it works better for you than it did for me. SF Bay is pretty breezy which was the source of my problems.
Peter