I spoke at length to the dealer shop foreman about preventative maintenance.
(Don't know anything about the sedan but you can probably extrapolate)
It is particularly difficult on the E61/wagon, because the two rear drain tubes are under the fixed glass at the very rear of the cassette and require the headliner removed etc to get to.
The two front tubes are accessible and as sunroof drain tubes go, pretty tiny (assume the rears are the same).
If you have one of them clogged and the car on an incline with the clogged one lower, you are in trouble.
My dealer was not willing to clean the tubes with every oil change.
However, we did come up with a way to self diagnose if they need cleaning.
Using a SMALL watering can, park the car on an incline nose down. Put water through the each front tube and check it comes out promptly behind the front wheels.
Now put the car on the incline tail down (nose up). You can't reach the rear drains but you can pour it into each side of the drain channel on the outer edge of the cassette (typically the dirty bit). The water should run down each side back to the drain tube and come out in front (?) of the each rear wheel.
So I figure I'll do this once a year or so, and if it is clogged, have the dealer clean them out. The only issue I can see here is it might be difficult to detect a partial clog.
I was also given the "don't park under a tree" but in the Pacific NW that is difficult to avoid.
Now that I understand how it all works, it is pretty clear to me this is a design flaw.
Design a really poor sunroof drain system, that clogs easily. Then have it so when it overflows the water drains into the trunk bay with the most expensive electronics in the car. And then make it somewhere where the owner can't detect it is full of water until it is too late.
My Subaru Forester is parked under the same trees, and never an issue with clogging.
My final joke on the subject: what the E61 really needs is a BILGE PUMP.
I didn't push the dealer on their position that the bulletin only covers the older sunroof designs. (by my read it also covers clogging on 08 - I was not able to get a copy of an 08 warranty RO from anyone here)