Hey, good question! Sand to lagoon, sand to reef and sand to grass all paint with Godot’s terrain tool: lay sand first, then paint water or reef over it and the edges and corners fill in on their own. One tip: every edge goes from sand to something, so leave a strip of sand between water, reef and grass.
The pier is the exception. Right now you place it from its guide, because Godot’s terrain brush can’t draw the pier’s front face under the deck. (In Tiled the pier paints with the brush too.) I’m working on a free update that adds ready-made pier stamps to the Godot TileSet, so you can drop straight sections, corners and ends in one click instead of tile by tile.