It's possible those areas are part of the ventilation system. Somewhere there's a drawing that describes the airflow through the cabin and I think there are arrows that exit near those areas on the sedan. You can see the vents in pics from Army's rebuild thread in post #27. In the wagon the vents may be in that last pillar (D pillar?)

It is possible that water is leaking there in there, but there are other suspects as well for filling the wheelwell: the sunroof drains, the antenna gasket and even the trim retainers for the side molding strip, or all the above.

I can't really see the mystery rubber in the pics. I'll throw out another plug today for searching chad300tdt's bodywork threads, particularly for the wagons.