I've had the same problem with my 2003 TD4 and after watching the video https://www.youtube.com/watch?v=f4EtsYTJ8uE I did the same thing with the hose pipe from below and water came up. I sealed all around the top joints of the toolbox well with clear silicon, plus the screw fixing holes. I also went under the car and painted everything in the area with underbody sealer.
After driving through loads of deep puddles no more water came in from below. However, a few days ago we had a heavy downpour when the car was stationary and the toolbox had a couple of inches of water in it again. I then took off the plastic trim fitted to the roof above the window and saw that the seals there are rotted. I think that must be the problem. Let me know if you have any luck because I don't know where I can buy them. Cheers Bob

the back door seal is known to let water in .

i had that problem drove mad trying to find it tried everything
with hose pipe it turned out it was getting in a vent on the rear
n/side wing behind the panel in the boot not sure what the vent
is for but someone will come along with a answer

if it is getting in round about's where the vent is then check behind and look if the sunroof (if it has one) drain pipe has not come off as it fits onto the bit going out of the car. hope this helps