Russ, the gasket along the bottom of the penthouse doesn’t seal well on the front above the cab because of those roof channels - the rubber on the gasket doesn’t seat well because it rests mostly on the higher ridge of the roof…so yes, if you are parked on a slope where the front of the van is higher than the rear any water will drain inside. Same would apply if you are driving in rain, the wind will blow the water under.
Years ago I placed self adhesive neoprene pads in those channels (cut the edges at an angle to accommodate the angle of the channel). Now when my top comes down the rubber gasket on the roof rests nicely across the neoprene so I don’t get any water intrusion- hardly get any dust or debris inside either.
I can’t remember if I order 1/2” or 3/4” pads - they just need to stick out above the roof line by 3/8” or so to gain a good seal. I did cut the pads down so they were about 3” deep (about 1/2” in front of the gasket and the rest sets back underneath). Only did this because the roof doesn’t come down exactly in the same location (pretty close, but some deviation based on the angle of the van when the top is lowered).
Hope that helps.