I've used the modutop bars on mine for 9 years on a regular basis for roof boxes and ladders etc and it's never let a drop in.
Off camping in a couple of weeks with the roof box on there.
Some may have developed leaks where the rubber seal has perished, but I don't think it's linked to using the bars personally.
Our modutopped 04 Berlingo was used and abused for the 8 years we had it and our local Citroen specialist was horrified to hear this tale of our touring holliday in France.
After a superb and trouble free month in Northern France from Brittany to the low countries we returned to our ferry port for the last night and the hotel we had booked said it had secure parking. Tired as we were, we failed completely to notice the restricted headroom sign and parked with a peculiar swishing sound in the underground car park. Leaving the car we could follow the groove in the roof which marked our course of entry and decided that we should worry about the exit and the top box tomorrow.
The morning after we got up early in case we had to go back out the in door as the exit seemed even lower, but having parked back out in the sunlight there was no damage to the contents but the top box looked more like a squashed frog than ever, and a heavily stood on one at that.
My independent dealer said we were lucky not to have been boarding the ferry with the roof balanced on our heads in the car. The top box had been filled with camping gear, bed rolls and sleeping bags and must have been fairly weighty in its own right but the only lasting damage was the jaunty angle the squashed frog adopted till a hair dryer loostened it back to a little of its previous incarnation once we got home. How much pressure the roof had taken underground doesn't bear thinking about.
After such a misadventure you would have expected the worst regarding leaks but it wasn't till years later we found that the roof suddenly developed a huge leak right over the front passenger seat. A cursory inspection showed the culprit was a pine needle pushed under the rubber seal from a Christmas tree and its removal was all that was needed to stop the problem.