Hi Fellow Weirdo,
I wouldn't have thought it would be a problem if your pen flooded,if anything,the pigs will love wallowing in it,especially when it's hot in the summer. When you first get your pigs,you could easily strip-graze them across the pen so there's always a dry bit for them,by the time they're big enough to need the whole pen,the risk of flooding will have passed.
As for the pebbles,the pigs will root them out and dive in under them eventually. Every night just before sunset last year,I walked around the pigpen with a bucket picking up stones,wire,glass and even unexploded ammunition that the pigs had managed to bring to the surface. There was a fair old heap by the time they went to the freezer....... Ree