The carpet has a plastic membrane underneath it on the Multispace. Water eventually finds its way under this, but drilling a hole in the bottom of the well isn't an ideal solution. Even if you drilled a hole right through, the damp carpets will become a problem. The Berlingo van has a rubber grommet in each rear footwell which can be pushed up from outside, but the water won't drain away as fast as you would like.
Some have fitted a boot liner that will contain any spills. With the Multispace, the rear seat is mounted on the main cargo area floor and folds up on itself. It would be easy to fit a boot liner that could be taken out with everything else if the rear seats are needed for family transport.
Water will be running underneath the rear seat (if you haven't removed it) and running into the footwells. The rear seat is mounted above the fuel tank. The floor is one continous sheet to the rear doors. There are no joins as it is one continous floor pan.