You end up becoming powerful enough to stroll through swamps and mountains, even the plains, and just putting off attacks while you build. The workbenches stop random spawns within their radius also contributes to the feelings you describe. As far as my docks went I ended up embedding workbenches inside the stone blocks as part of their design then adding some stakes underwater as they futilely threw themselves into that area of the water constantly. Not because greydwarves were any threat to me by then but because it was just annoying not to be able to sleep right away or listen to them.

Regarding the water changes, I built on calm days and ended up using the water level to build a wet dock that works great with some effort and using the hoe to build up land underwater for the foundation. Convenient to launch ships or destroy them to transport through portals without fear of losing the nails.