I noticed in the map making manual that you shouldn't place rivers underwater. Is this an aesthetic thing since you can still see the river, or is there an actual gameplay reason for this? I ask because as of now the only way to have a river start at a lake is to start it in the lake, since it won't connect otherwise. Would having underwater river segments disqualify a map from the creation contest? 

As long as the game validates they should be fine, I think you wouldn't want to just because it might look a little weird. Plus it would mean that technologies that buff river tiles might make harbors really good, but I think as long as you follow the instructions in the contest on how to submit it you should be fine.