The Vanagon system has outside air entering at all times. The only way to shut it off is to have the top two levers full left and the bottom two full right to send all the air to the dash ducts. Then close the dash ducts. You should find foam seals inside the ducts. These compress and deteriorate over time and may just need replacing. Self-stick strips from the hardware store.
The temp lever "should" cut off water flow to the heater core. If it works, then you are only have leakage of fresh outside air into the van.
The one I would dread is the flap that diverts air from foot to dash. If it goes, you can't force all the air to the dash vents, the only ones that can be shut off. I think I'd be cutting some of the block foam to stuff up into the footwell ducts during the summer rather than pulling the duct box apart.
Side note -- something I've never really figured out. On mine, when you divert air from up (3rd lever right) to the footwells, the first inch as I move the lever back left, which actually has a little mark in the bar, will send hot air to the feet by the pedals, but as I continue moving the lever left, it then sends it to the ducts coming out the front of the panel below the center of the dash in front of the sheft lever. Personally, I find I'm warmer with it on my feet, which should only be about ¼ of the heat down and the rest to the dash.
The German Enigma Code of WW II was easier to decipher than a VW heat system!
Regarding the through door ducting, I'd suspect that horizontal duct under the dash feeds into the A piller at the door hinge, thus the hollow A piller becomes part of the duct. Of course we also have to remember that the heat system may be ducted for some other market (the Type II Baywindows were available with heater vans that cut into ductwork in other markets than N. Amer.) and we've just got the remnants where it was cheaper to add the boots & foam rubber than block the system. See paragraph above!