RE: Stock setup on starting battery compartment
On my '90 Westy (and IIRC also on my previous '85) the starting battery has
a nipple on top  that attaches to a hose that goes out through one of the
holes in the battery compartment, thus venting any fumes or gas from the
battery to the outside.  I'm going to speculate that most Vanagons out there
now are missing that hose and that (mine included) the cover, with it's
seal, is not screwed down to make a seal.  And I also have a vague
recollection of seeing a hole in the aux battery compartment to allow the
same kind of vent hose to be installed.  But of note is the fact that the
cover for the aux battery under the drivers seat is NOT sealed but hinged
with a latch, not held down by screws like the starting battery.