I don't claim to have all the answers to your question,  but I do know that
the engine compartment in a rear engine car is a very dirty environment!  The
dust kicked up bythe front of the car ends up in the engine compartment.

The air intake up the body panel eliminates that problem...  The Syncro even
claims there is a snorkle attached that allows intake air to come from near
eye level.  However, I would be very surprised if the engine electrics could
handle water at butt level.

The air cooled bus had rubber seals and sheetmetal around the engine
compartment and if in good shape would keep dust and debris from entering the
air filter.It also  prevented engine heat from re-entering the engine cooling
system.

If I were you, I'd do everything I could to return the intake air to that
original location.

Good Luck,
Curt Long
87 GL Syncro Westy
71 Big Bore/Stroke Camper
87 Acura Legend
94 GAS GAS Trials bike