I don't know which Keystoker direct vent unit you're working with but here's the venting instructions for the Koker 160,000 btu furnace:
3. Select a position on a solid level surface. On non-masonry floors, use an approved fireproof protector under stove. Maintain 16” clearance from side of stove to combustibles. Maintain 6” clearance from 4” pipe to combustible. Clearance from 6” black wall pass thru pipe is 0” to combustibles.
The 4" pipe referred to is the single wall vent pipe. You only need 6" clearance from your floor joists or any other combustibles.
If you go out of the house thru your rim joist you do need the 6" pipe around the 4" vent.