Drill a hole in the boot
I too was frustrated as the boot got flooded in my 545i Touring (E61). It is the left back tube that comes of at the top. Twice it has been refitted. Now I have drilled a hole in the boot at the lowest point, so water can drain out. Not very pretty or advanced but cheaper than paying for fried electronics. I now have to avoid driving in ponds - I will have to live with that. Any other risk ?
All the best