I had also made this assumption about seal D but it has two very specific areas where there is a gap underneath (no adhesive) that allows water from area Y to drain under the seal, location A, into area B. This gap is present on both sides of the van. You will over time see an accumulation of dirt (You can see some in your photo). You should clean this dirt away every so often.
If you want to avoid water getting into this area when the roof is closed you need to investigate the seal between the fixed roof, area Y, and the elevating roof part. This seal is attached to the front edge of the elevating roof. Is the lip of the seal making good contact with the location A? If not it will leak along the path I have described.
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