Plugging Knotholes

and only need to get a finish that's close to the grain/rough sawn pattern, I'd use plugs of whatever kind you wish (pvc trim scraps, dowells, other-and epoxy.  Take a scrap roughly the same shape (if round-drill out plugs with a hole saw).  Get enough of them ready so you can set them b/4 the epoxy hardens.  Apply some epoxy around the inside edge of the hole-butter the edge of the plug.  Place the plug in the hole-register it to the rest of the board using something flat to press in the plug till it's flush with the board.

Once hardened-apply aanother final covering which you can add grain marks to dragging a small knife across it.  Or, if you get lucky-the final moments as it starts to take off-just dragging a putty knife across it flat will produce a rough sawn appearance.

Small holes-fill with Urethane caulk and texture it to match the boards appearance.