Does this happen on the 317s O L Leigh? I would imagine it does.
A little but not massively.
The problem is the amount of water that can collect in the rain channels on the roof and in the pantograph well, especially when you're not going very fast. When you brake or accelerate this all flows one way or the other over the coach ends and down between the vehicles or over the cab fronts and down the windscreen (and in the side droplight as well if you're foolish enough to have left it open). Sometimes it's just too much for the corridor rain screens to deal with and you do get a wet floor between coaches.
However, I've never experience flooding of the scale being alluded to by the OP on a Cl317. Mind you, as I said above, I have been PASS on quite a few "Bins" where the rain screens were either missing or not properly fitted and you could see the sky through the gaps.
I'm regularly on the Class 320s and never notice any leaking, although they obviously don't have any toilets.
It's not the toilets that are causing the flooding if the water is coming down over the roof. Even then, flooded toilets are usually caused by vandalism such as toilets or sink drains blocked with tissue.
O L Leigh