Well I spoke in haste. I dug up my notes and this is what I wrote about how I think the ground type and heights interact:
Groundtypes: shown in the background is a beach running from top left to bottom right, with land in the upper right and sea at the lower left.
Heights: Overlayed on it is a piece of the triangulated network that makes up the 3D surface. The height values in the tga and hgt are the elevations at its nodes. As such they are placed under the center of the ground type tiles.
Now imagine the height nodes under the beach tiles being +1 and the nodes under the sea being -1. In this case the coastline* will run along the pink line. I think it should be closer to or under the dark blue line. That is what I do in the hgt anyway by simply setting the height to 0 under the protruding beach tiles.
In the tga you can approach this in several ways: drop the height under the offending beach tiles to 0 or lower the height under the adjacent sea tiles. Vanilla does the latter btw: A value of (1,1,1) corresponds to about +20m while a value of (0,0,255) corresponds to -30.
* the intersection of the flat 0 altitude plane and the 3D wireframe.





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