Water does seem to pass through the seal on the sunroof glass they do tend to rust over the years. Once it does, if it collects a certain amount it starts to roll of into the nearest runner (hole/tube). If the runner is clear then it keeps running that way. Over time it tends to build up gunk and so fourth while you open and close your sunroof. Eventually it gets clogged or clogged enough to where the water can't flow consistently. If you open your sunroof you'll notice from the top and bottom that it seems to have a lip, a little high rise, to keep the water from coming in the car. Once those tubes are too clogged the water starts to go pass that, hence bringing water inside the car (headliner, seats, etc).

The only solution is clearing out those tubes. If you clear out those tubes completely (hearing tons of air coming out the wheel areas) you shouldn't have this problem continuing. If it continues then you have a rust build up between the seal on the glass somewhere. I replaced the glass and seal thinking that was it on the 2g I used to own and it ended up being the tube(s) were clogged.