One of the first things that I did to our van was to replace the seals.
When I did I took off the luggage rack and the metal roof under the rack is
the top of the standard vanagon.    There are several mounting straps that
hold the rack on and they are fastened to the roof and then the rack is
fastened to them with the large flat faced screws that you see on the rack.
It is also held in back with three screws that are seen when you put up the
pop top and look at the area between the top and the rack.    If I'm not
mistaken these are the only ones that could leak and when you remove the
nuts on these you have to be very careful and not let them drop down as you
then have to remove the headliner to replace them.    I carefully held these
up in place and then put additional sealer around them.   The reason I bring
this up is sooner or later most people end up replacing their seals and when
I did I was appalled by what the metal top looked like under the rack.
While I had the rack off I completely cleaned and double waxed the roof
area.
    As far as the water drainage goes it simply goes through the holes and
onto the cab roof and either out a small area under the front corner seals
or out the rear of the rack at each rear corner.    The only way that I can
see any water getting into the area of the headliner would be through one of
the three mounting holes at the rear.  That's the main reason I put
additional sealer on them.
    Hope some of this helps you

Dick & Janette Smith
Norwich, NY
85 Westy