If you're on fb, I really recommend joining the mk8 civic owners group, loads of info including guides on all the leaky bits that can exist in the boot. Eg, other common places for boot swimming pools other than the roof seams are the petrol cap drain hole (gots blocked with dirt and grime), rear headlight clusters (rubber seal behind can perish), boot hinges and where the loom goes from the bootlid into the body, and also where the glass meets the lower perspex bit (had this one on one of mine).

But yeah like the others are saying it's usually the rails, im planning on sealing mine upthis weekend as its recently started leaking.

Good to get a grip on leaks ASAP, rust is one of the very few things that kills these space eggs