It's not clear in the pic but we do get the fresh air from the same place as
the Vanagon (which has the air box and muffler in aproximately the same
locations I might add) we run a short piece of large diameter hose from the
airbox and out past that cardboard partition so that it is getting nice cool
air from the passenger side rear vent (just like the waterboxer).
We did run it for a little while getting the warm engine compartment air when
we were first getting the engine running and it ran pretty good but adding
the fresh air hose really helped.
Also the 5-cylinder engine doesn't seem to run as warm as the waterboxer (it
has to do with how the exhaust system is setup).  The 5-cylinder setup allows
way more space between the motor and the exhaust piping (so there is more air
flow over the pipes and therefore actually less heat in the engine
compartment itself).
Just FYI.
Ken Wilford
Van-Again
John 3:16