1) I agree that most rivers should start on higher ground and flow downward to the sea.

2) it would be a very, very unusual place to be unable to build a dock between raising the underwater terrain a little (or a lot, a very good dock for any size boat can be made from simply editing the terrain and adding like stairs to get in from the water or some cosmetics) or hacking up the shore a bit. Couple that to long running horizontal ironwood beams and what can you not do dock-wise? If you have a sheer drop-off into deep water, that is difficult, but again, its also quite rare, most land has a 1 viking tall shore out for 10M or so. Maybe it depends on how you define 'proper' dock. All I want is a ship sized area of land that is just barely deep enough to walk in during calm weather -- i will build the ship here and break it apart here, with no risk of losing mats because its shallow. That is beside a raised area that is out of the water a few clicks (typically a long thin strip) so I can jump on and off the boat to shore. And as said I tend to run stone stairs into the water so i can get up there if I fall in or something, and after that its all cosmetics.

3) yea this is a do-over of all water in the game, from what I can estimate.