Hi Gixxer,
Keep in mind with my experience, i'm in exactly the best climate for bringing forward issues of moisture ingress(Ireland & the U.K.) so i guess these problems will not affect everyone to the same extent.
1. The body vents. Seems to be a common issue. Will manifest itself as water found below the spare wheel. You will need to remove everything maybe even the spare to see it. The vents aren't a tight fit in their cutout. The path for drain water passes straight over them. When static, the vent seal sits nicely and prevents ingress to the boot. But when driving(i believe) the vibration on the vents allows water to come in. Proved by gently vibrating them by hand while in the presence of rain.
Solution, silicone seal them in place.
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2. The VW Boot handle drain pipe issue is very common. While searching for 'Water in VW Golf VII Boot', i found it was a potential cause. I went out and checked and just like everyone else, mine was perished.
Solution, Replace it. £10 i think.
3. The door leak is also very common. It may/may not surprise you(It did surprise me), water is designed to pass through the metal outer and inner skins of each door. It goes from either end of the window glass seal where it is
not water tight(maybe by design), down through the door, over the door locks and window regulators into the bottom of the door where it passes outside via a Forward and a mid drain hole which looks like a slot.
The seals on the speakers rot, i'm not sure after how long, my car is 5 years old. This creates a path for the water to come from between the inner and outer skin to enter the interior and pool in the footwell.
All 4 speaker seals were rotten on the lower most portion of each speaker, however, only the rear really had much water enter the car. The right rear was awful. The rear door design seems to cause any rainwater that enters the 2 skins to take a specific path that takes it directly to the speaker!! When your seal goes, it's coming in. It's ugly as F*ck.
Solution(for me), silicone, put a bead inside that directs this water from above the speaker around it, think along the lines of what your eyebrow does for your eye, that kinda shape.
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I will say these are all my opinions and can't say 100% that i'm correct, just that these are the fixes i applied and time will tell if they are good enough or if there is unintended consequences.