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The foam you are describing is likely there for noise abatement in a cavity where Honda does NOT expect water entry. Foam, whether closed or open cell will retain water and cause rust over time - an issue which OEM pay close attention to.Ref: "A Pillar- B Pillar Found", also, "Any body Men out there to track a leak?"
4.5 inches of snow in April in New England, day before last. My entire headliner and rear seat assembly, bulkhead insulation, all rear interior trim are out, subwoofer, everything. The water is leaking from both corners of the outer rear cab bulkhead. Weirdly, there is foam rubber stuffed in the lower corners, both sides of the double walled structure. On the left, the cable for the fuel door is going thru a slash in the foam to perhaps keep it from rattling. On the right side no cable, just the foam stuffed there. Both of these were wet when I yanked them out 2 days ago. In the middle it's dry, and no sign of leakage, it looks like new. Also, no foam there??
By noon yesterday the April sun had melted and dried all the snow from the storm over night. All except the snow in the bed, which was facing north and shaded from the sun. So, no source of water from anywhere but the bed. Sure enough, the water was oozing in from the rear bulkhead wall, both corners. IT HAS TO BE FROM THE BED!
OK, how do I get there? I'll try the wheel wells this weekend. I know already that the lower bed is impossible to get out unless you had 4 guys or an engine hoist, etc. I tried doing that before- very heavy and binding- especially at the storage trough.
The bed is about 20" below the lower edge of the rear window, which if you go inside the cab the rear cab wall goes down about 28." Those corners with the foam rubber are the low point.
I really wonder if Honda put the foam in there to absorb incidental water from the bed. Why else wouldn't they put foam in the middle of the bed? The low point gets the water- so just put "sponges" at the low corners. I really don't think this is a sound insulation thing, as there are all kinds of layers of that in that area, plastic/fiberglass insulation wall, subwoofer case- (pretty impressive!), heavy and thickly upholstered seats with all kinds of foam, cloth, and thick leather and vinyl.
I will fix this sucker!!
Help body guys!! Help!
IF you suspect water collecting in the bed is finding its way into the interior cab, I would suggest the route it is taking is unexpected from a design perspective. Its a total guess on my part but... the weep holes under the cab/bed wall might be plugged with debris, causing water to find its way to an "un-managed" exit point. There are 8 weep holes at the low point of the forward bed bottom, where an upward lip is molded to keep water from overflowing. See image below.

It would be very easy to inspect those weep holes. If blocked, clear them and test results.
Even if they are blocked, your issue suggests a seal or panel joint is coming undone. The entire cab/frame/bed interface *should be* as close to water proof as could be mass produced, so its likely the concentration of water in your environment is showing you a defect somewhere down under.
Assuming you've already inspected all passages to the interior, such as grommets and body plugs, to may have panel leaks - why that might be could be corrosion, an initial OEM defect in assembly or the result of some sort of traffic incident in the RL's history?

Keep us posted and best of luck!