For the OP, in my Audis and VWs as well as currently in the Durango there is a setup for in cabin filter that goes in the cowl, outside of the cabin. The filters can be purchased with activated charcoal and mold inhibitors. I even installed the Durango/Cherokee units in the JKU for when running the AC and vents. This setup controls a lot of the pollen and smells that are pulled through by the HVAC system. around 12-24 dollars depending on brand and features. My current TJ doesn't even have an enclosure/cover under the cowl for the HVAC air inlet and when I turn on the defrost whatever falls through the mesh in the cowl finds its way the system and blows to the windshield. Bees, bugs, pollen, small leafs, you name it.
I am going to install a setup to prevent that and keep water out as well. Obviously running without doors and top will be pointless if one is trying to keep the air better, but for those frosty or wet morning and using the heat it will be nice to have some clean air pushing through.
Activated charcoal will do a lot of good not just for scents, but also for some of the nasty fumes.