First the reason why this happens. Then I'll give you a solution
Altitude constraints in the Surface Layer are based on the "position in texture/terrain" (a.k.a. texture coordinates), not the final displaced position. This is so that colour and displacement are based on the same altitude constraints, and displacements don't have access to the final displaced position and can only be based on the texture/terrain coordinates.
The texture coordinates are computed by the Compute Terrain and are a slightly smoothed version of the actual terrain. That allows the difference between actual terrain and computed terrain to be used by other special effects such as the "intersect underlying" feature.
Workaround: The Distribution Shader has an "altitude key" setting which allows you to choose between "position in texture/terrain" and "final position". Final position should give you something that aligns with the shoreline. You can use a Distribution Shader as a blend shader for your wetness layer.
I plan to add the same option to the Surface Layer in future.
Any remaining discrepancy between altitude constraints and water level can be explained by the difference between 'Y' and 'altitude'. The water level is specified by altitude. Coordinate readouts in the 3D Preview are 'Y' coordinates, which may be slightly different from the altitude due to planet curvature.
Matt