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'97 Type SH 2.2 VTi 185BHP
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Unlike the other threads, I believe this is has a less common cause, of which I'm yet to determine.

For context:
I changed the taillight gaskets a couple of months ago, as I was getting water coming in through the rear left, which was collecting around the spare, near the drain plugs.
Since then, I noticed a small gap between the metal of the boot just above the rear left, which due to rust, had moved apart slightly, letting water in (see below picture). I sealed this using some sealant, and again, it's been dry since.
Hood Automotive lighting Automotive tire Fluid Car


Today, I had a look, after some heavy rain, and the wooden spare cover was wet, again on the left. I pulled the liner away, and found a pool of water had collected near the vent (I've since dried it out in the below picture).
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I've checked the drainage from the sun roof by pouring some water over it, and I can see water coming through the drain hose and onto the floor perfectly fine (I had the sunroof shut, so only a few drops were actually coming through the drain hose. I did pull it out to inspect it, and it is not blocked.
I also checked the drain just under the fuel filler cap, which again drains without water ingress into the boot.
The surrounding body panels showed no black streaks of dirt carried by water ingress, similar to that in the first image.

The only evidence I can see is that the yellow looking seal towards the left of the photo was damp, and did have some black dirt, but the entire panel was covered in condensation, so it's not a confirmed indicator. I could not see any spots where water droplets were forming, nor where the point of ingress could be, unless it is that joint itself.

Any ideas?
 

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Unlike the other threads, I believe this is has a less common cause, of which I'm yet to determine.

For context:
I changed the taillight gaskets a couple of months ago, as I was getting water coming in through the rear left, which was collecting around the spare, near the drain plugs.
Since then, I noticed a small gap between the metal of the boot just above the rear left, which due to rust, had moved apart slightly, letting water in (see below picture). I sealed this using some sealant, and again, it's been dry since.
View attachment 32184

Today, I had a look, after some heavy rain, and the wooden spare cover was wet, again on the left. I pulled the liner away, and found a pool of water had collected near the vent (I've since dried it out in the below picture).
View attachment 32185

I've checked the drainage from the sun roof by pouring some water over it, and I can see water coming through the drain hose and onto the floor perfectly fine (I had the sunroof shut, so only a few drops were actually coming through the drain hose. I did pull it out to inspect it, and it is not blocked.
I also checked the drain just under the fuel filler cap, which again drains without water ingress into the boot.
The surrounding body panels showed no black streaks of dirt carried by water ingress, similar to that in the first image.

The only evidence I can see is that the yellow looking seal towards the left of the photo was damp, and did have some black dirt, but the entire panel was covered in condensation, so it's not a confirmed indicator. I could not see any spots where water droplets were forming, nor where the point of ingress could be, unless it is that joint itself.

Any ideas?
If the trunk door seal is good money then I'd look into adjusting the actual trunk door...you could possibly adjust the locking latch lower for a tighter seal but don't overkill it. The trunk door could be misaligned or it could just be the seal. One first things I replaced on my second 5thgen was the trunk seal, I ordered it online from Honda. That leak will ruin your interior with a moldy smell.
 

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LOL...I have EXACTLY the same problem...i can see the water at that "connection" you have tried to seal,i did exactly the same thing. i dont think its anything to do with the trunkseal or even around that seal(corossion, pinhole, etc) i tried for MONTHS to find the leak...is it up on the roof...? back window seal? i finally gave up after "sealing"the roof down basically...if i had to guess id say its a body seam leak around the B pillar somewhere..i know my car was hit there early in its life so i guessed that didnt help, but it has EXACTLY the same leak on the other side, i see a few people have had this, its hard to realize exactly where it comes from (or ends up)..i didnt have the rust you had to help show me. i finally drilled a hole in the 2 sides of the trunk (below jackmount) and no more pooling water, but i really hated giving up and doing that...but it kinda works

your right...this is the leak no one really understands...ie less common
 

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Put a beat of silicone or some other form of sealant beneath the trunk seal and inspect the rest of the seams around the back of the trunk. I had this issue as well and put an added bead of sealant over all of the seams. The only water I see now is due to a tail lamp not making full contact after an accident over 15 years ago.
 

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I took the entire trunk seal off and did that,thought it might be a pinhole leak UNDER the trunk seal, sealed the trunk seal to lip.....no luck, i think the leak is higher up, its a VERY specific leak, i sealed the "actual leak" and then i could see where it was coming from , that was a revelation in itself, but i think the water is under some small pressure so its not as simple as blobbing silicone on it, it just kind of bled through/around the silicone,...it leaks right at the round body tab right above the long dirt streak in the first picture, it beat me, i gave up
 
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