After rewriting the tileengine again, I get this:

You can see a blue circle at the mouse pointer - that is an editor function:
you select 1 edge of the tile and change height or texture.
No more need to select from 100s of filters.
This version uses 4 texture units (nr 4 is reserved for fow, etc)
The horizontal lines are filtering errors. I must sacrife at least 4 of the src textures.
That means we have 28 textures in the atlas left.