I haven’t seen this subject recently so here it goes..... I store my work gear in my trunk. Twice in the last month I found it soaking wet after a big rain. Nothing when it’s a normal rain. Rubber seal looks good. Any ideas why it’s leaking?
Noticed the same in mind, particularly on the right side of the trunk. I pulled back the carpeting on the rear right panel (inside the rear quarter panel) and found a big foam/rubber gommet with a tube for the sunroof drain running through it. The grommet had been pulled out of it's seat for some reason and was allowing water to run into the trunk. Re-seated the grommet and it's be perfectly dry in the trunk since (this was months ago). I wouldn't be surprised if you've got the same issue.
mine was leaking around the center brake light, but there are many places that might leak, like sunroof drains. If you're not claustrophobic and you have a friend you can trust, then remove the trunk liner, get in the trunk with a good flashlight and have someone spray water on the car. Just by removing the trunk liner you might see rust or water stains where the leak is.